Method and a device for the evaluation of biopolymer fitness

ABSTRACT

A Method for identifying one or a small number of molecules, especially in a dilution of ≦1 μM, using laser excited FCS with measuring times ≦500 ms and short diffusion paths of the molecules to be analyzed, wherein the measurement is performed in small volume units of preferably ≦10 −14  l, by determining material-specific parameters which are determined by luminescence measurements of molecules to be examined. 
     The device which can be preferably used for performing the method according to the invention is a per se known system of microscope optics for laser focusing for fluorescence excitation in a small measuring compartment of a very diluted solution and for imaging the emitted light in the subsequent measurement through confocal imaging wherein at least one system of optics with high numerical aperture of preferably ≧1.2 N.A. is employed, the light quantity is limited by a confocally arranged pinhole aperture in the object plane behind the microscope objective, and the measuring compartment is positioned at a distance of between 0 and 1000 μm from the observation objective.

This is a divisional of Ser. No. 09/021,410, filed, Feb. 10, 1998, U.S.Pat. No. 6,582,903, which is a divisional of Ser. No. 08/491,888, filed,Oct. 10, 1995, abandoned, which is a 371 of PCT/EP94/00117, filed Jan.18, 1994.

The object of the present invention is a method for identifying one or asmall number of molecules, especially in a dilution of ≦1 μM, usinglaser excited fluorescence correlation spectroscopy, the use of saidmethod in particular applications, as well as a device for performingthe method according to the invention.

In recent years, analysis of biologically active molecules has beenconstantly improved in terms of specificity and sensitivity andsupplemented by basically novel techniques. In this context, we mayrefer to cloning methods or the methods of enzyme-based amplification ofgenetic material to amplify single cells or molecules to such a numberthat they become apt to conventional analysis. In many cases, however,it would be more advantageous if analytic methods were sufficientlysensitive to qualitatively and quantitatively apply directly to singlemolecules or ensembles of a few molecules.

Electron microscopy, for instance, is a technique that can detect singlemolecules. Thus, attempts are made to sequence single DNA molecules bymeans of tunnel electron microscopy. This is very laborious, however.

Beyond the mere analysis of single molecules, information about stateparameters of the molecules, such as their conformations andinteractions with other molecules or molecular structures, are importantin many fields.

Modern methods of evolutive biological engineering are concerned withhighly complex collectives of molecules. Their object is to identifymolecules having specific properties of interaction with targetstructures, that is to measure a particular fitness with respect to adesired function. Such fitness can be reduced to thermodynamicparameters such as binding constants or rate constants.

Sometimes it is less critical for the solution of particular problems toincrease the sensitivity of an assay method, for instance when themolecule to be analyzed is present only in small concentrations. Rather,a very large number of samples which have to be analyzed more or lesssimultaneously must be coped with. If for instance 10⁶ analyses have tobe performed within a period of hours, it is obvious that only ananalytic method can be considered where the samples can be measured andevaluated within a period of about 1 ms to 1 s as a maximum. The problemunderlying the invention is, inter alia, to provide a method which,beyond the mere detection of single molecules, allows for informationsabout their specific interactions with other molecules or molecularstructures to be obtained. Moreover, a very large number of samples isto be analyzed virtually simultaneously.

The method according to the invention is based on a luminescencedetection and makes use of a technique which is known per se under thename of fluorescence correlation spectroscopy (FCS). Chromophorousmolecular structures having fluorescence properties can be used toobtain information about the molecular environment of a chromophorousligand. Rotational diffusion and translational diffusion of aluminophore may be measured as well as different paths of energytransfer to interacting molecules, chemical kinetics and the lifetime ofexcited states.

Based on physicochemical phenomena known per se, the method according tothe invention provides novel solutions, making use of spectroscopicmeasuring parameters, for obtaining information from single molecules ora small number of molecules about the nature of said molecules as wellas information about their fitness with respect to a particularinteractional function or about the populations of different states of aluminophore which are defined with respect to one molecule.

To date, the method of fluorescence correlation spectroscopy as pursuedby the groups of D. Magde (Elson, E. L. & Magde, D. (1974) Fluorescencecorrelation spectroscopy; Conceptional basis and theory; Biopolymers 13,1-27) and R. Rigler (Ehrenberg, M. & Rigler, R. (1974) RotationalBrownian motion and fluorescence intensity fluctuations; Chem. Phys. 4,390-401) for nearly twenty years could not be technically incorporatedinto a practicable analytical method without difficulty. It has not beenpossible to meet the above mentioned requirements with respect ofmeasuring times and the light induced bleaching (photobleaching) of thedyes. Rigler et al. were able to determine rotational times ofmolecules. Magde et al. were able to determine some chemical reactionconstants through fluctuation times.

The principle of measurement of FCS is to measure fluorophorousmolecules in extremely diluted solutions (≦10 nM) by exposing arelatively small volume element of the solution to the intense excitinglight of a laser. Only the molecules having a corresponding excitingspectrum which are present in this same volume are excited by the light.Then, an image of the emitted fluorescence from this volume element canbe formed on a photomultiplier with high sensitivity. If the solutionsare diluted, significant variations of the concentration of themolecules present in the respective volume element will arise.

In particular, very diluted solutions will exhibit a Poissondistribution of the number of molecules which are simultaneously presentwithin the volume element in a certain period of time. A molecule whichhas once diffused into the volume element will leave the volume elementagain within an average yet characteristic, for this type of molecule,period of time according to its characteristic diffusion rate(translational) and hence will not be observable any longer.

Now, if the luminescence of one and the same molecule can be excitedmany times during its average dwelling time within the respectiveobservation element, many luminescence signals from this molecule can bedetected. In other words, the probability that a molecule which has oncediffused into the observation element can be excited once more before itwill leave the volume element again is much greater in diluted solutionsthan would be true for a freshly entering molecule. Though this meansthat with a correspondingly great possibility the correspondingluminescence signal comes from one and the same molecule rather thanfrom a molecule which has freshly entered the element. Hence, acorrelation between the change with time of the incoming emissionsignals and the relative diffusion times of the molecular speciesinvolved can be established.

If the rotation of the polarization plane of exciting light and emittedlight is measured as a further parameter, then the rotational diffusioncoefficient of the molecules involved from which conclusions aboutmolecular weight, shape parameters or the surrounding matrix can beobtained may also be determined.

It becomes evident that it is even possible to detect single moleculesin diluted solutions by exciting one and the same molecule very often(several thousand times) and accumulating the corresponding luminescencesignal from many single measurements.

The realization of this measuring principle in practice was impeded bymany technical difficulties. Although modern laser technology wasemployed, the observation element was so large that biologicallyinteresting molecules having low translational diffusion coefficientswere present in the observation element during a period whose order ofmagnitude was about 50 ms. Such a period is significantly too largesince it causes strong bleaching of the respective dye ligands employedserving as the luminophore. Frequent excitation increases the chemicalreactivity of the luminophorous structure towards molecules of theenvironment, in particular oxygen, whereby the luminescence is alteredor quenched. Of course, photobleaching also leads directly to falsemeasuring data, since loss of luminescence (fluorescence) simulates themolecule's leaving the measuring element and a distinction bystandardizing the measuring method is hardly possible or can only beattained by unduly great technical expenditure.

To date, the wide practical realization of this measuring principle in agenerally applicable method was hence restricted to within narrow limitswhich will be overcome, however, by the method according to theinvention.

The critical breakthrough on the way to a routine method for the tasksof FCS as defined above according to the invention is achieved by theintroduction of ultrasmall measuring volumes (preferably 10⁻¹⁴−10⁻¹⁷ l),with total volumes of the sample being in the μl-range, the realizationof which requires the simultaneous use, according to the invention, ofparticular elements of excitation optics, single photon detection andsample handling. The measuring volume of the device described in theexperimental layouts is 2×10⁻¹⁶ l which is about 1000 times as small asthe measuring volumes described in the literature. Hence, theilluminated area has an approximate dimension of 0.1 μm. Supposing thatFCS provides correct data in particular for a concentration ofchromophorous molecules of 0.1-10 molecules per measuring elementvolume, the working concentration will be about 10⁻⁷−10⁻⁹ M.Measurements with maximum detection efficiency and backgrounddiscrimination can be technically realized by using confocal optics withhigh apertures in combination with single photon detection.

Binding constants can then be determined through translational diffusionif reaction time is slow compared with diffusion time. That means that aligand which is to be observed does not change or changes but hardly itsmolecular structure during its entering into the measuring compartmentand its leaving the same.

Otherwise only a correlation is measured describing the mixed state.Here again, the importance of the method according to the inventionusing very small measuring volumes becomes evident, since the dwellingtime of a molecule is about 1000 times shorter than with conventionalcompartments and hence opens up the usual dimensions of equilibriumconstants and rate constants of specific biological recognitionreactions, for example ligand/receptor interactions, for measurement.

1. The Significance of the Small Volume Elements According to theInvention

According to the invention, the significance of the small volumeelements for the performance of the methods according to the inventionand the uses thereof has different, experimentally distinguishableaspects.

The significance of the small volume elements should be seen under thefollowing aspects:

-   -   background scattered radiation, especially Raman radiation,    -   life of fluorescence dyes under light exposure,    -   short measuring times,    -   diffusion times of macromolecular complexes, viruses, cells,    -   integrity/preservation of the complexes not present in the        volume element, and    -   life of complexes during measurement.

BRIEF DESCRIPTION OF THE DRAWINGS

FIGS. 1 and 2 are flowcharts of receptor assays.

FIGS. 3 and 4 are schematic representations of FCS analyses usingmulti-well sheets.

FIG. 5 is a schematic representation illustrating the measurement ofmolecules using FMS.

FIG. 6 is a schematic representation illustrating the detection ofsingle molecules in an electric trap.

FIG. 7 is a schematic representation illustrating the tagging ofselected genotypes using FCS.

FIG. 8 is a flow chart illustrating the preparation of DNA/RNA ofFCS-selected genotypes.

FIG. 9 is a schematic representation illustrating the analysis ofmixtures following chromatographic separation.

FIG. 10 is a schematic representation illustrating a laser correlationmicroscope.

FIG. 11 is a flow chart illustrating the selection of possible assays.

FIG. 12 is a schematic representation illustrating an electrophoresiscell.

FIG. 13 is a schematic representation illustrating the field about alaser beam.

FIG. 14 is a schematic representation illustrating a measuring awaydevice including a prefocused laser beam.

FIG. 15 is a schematic representation illustrating a prefocusingappliance for a laser beam.

FIG. 16 is a schematic representation illustrating the arrangement of apreferred embodiment of the device according to the invention.

FIGS. 17 a, 17 b, 18 b, and 18 c are graphs of measurement results.

FIG. 19 is a flow chart illustrating FCS experiments performed inparallel.

FIGS. 20 a, 20 b, and 20 c are schematic representation illustratingembodiments of an electric trap according to the invention.

FIG. 21 a is a schematic representation illustrating molecular detectionaccording to the invention.

FIG. 21 b is a schematic representation illustrating a multi-elementdetector.

FIG. 22 is a schematic representation illustrating analysis of adisplacement experiment.

FIG. 23 is a schematic representation illustrating a method performedaccording to the invention.

FIGS. 24 a, 24 b, and 24 c are schematic representations of embodimentsof according to the invention.

FIG. 25 is a side view of a double microscope.

FIGS. 26 a, 26 b, 26 c, 27, 28 a, 28 b, 28 c, 29, 30, 31 a, and 31 b aregraphs depicting measurement results.

From the below explanations, it becomes evident that several parametershave positive effects in the sense desired according to the invention atthe same time in realizing small volume elements and, through acumulative effect, have resulted, according to the invention, in thenon-linear/exponential improvement of the methodology which has made thesolution of the problem according to the invention at all possible.

A signal-to-noise ratio of 1000 necessary for the measurement of singlemolecules is attained by small volume elements in the fl- andsub-fl-regions. The deterioration of this ratio follows the third powerof the increased radius of the measuring volume (r³). This behaviour wascompletely neglected in earlier experimental approaches in which a laserbeam illuminated the volume of a long column and virtually onlydiffusion in two dimensions out of the beam was analyzed.

If a larger volume is nevertheless to be analyzed for reasons ofmeasurement technique, then many small volume elements according to theinvention can be measured in parallel by multiarray detection and/ordifferent small space elements with distinct space coordinates can bemeasured in succession. The characteristics of the signal-to-noise ratiois maintained therein for each Gaussian space element as measuringvolume. According to the invention, each and every space element ispreferably illuminated confocally with prefocused exciting light as in asingle measurement of one space element and an image of the spaceelement is formed in the object plane by a pinhole aperture.

The methodological breakthrough of the technology to the safeidentification and measurement of single molecules and the possibilityof counting single molecules which is necessary for determiningequilibrium constants through the number of complexed and free ligandsin the measuring volume over a particular measuring period wasaccomplished by using measuring volumes of ≦10⁻¹⁴ l. This has becomepossible by employing, according to the invention, pinhole apertureswith diameters ≦100 μm, preferably with diameters ≦20 to 30 μm, as wellas by employing a prefocused laser excitation. With pinhole apertures ofthis dimension located in the object plane, a diameter of the Gaussianmeasuring volume of 0.33 μm to 0.5 μm can be reached at 60-foldmagnification. If optics with a different image scale are employed,correspondingly adapted pinhole apertures must be used. For freerhodamine, this means an average time for the diffusion out of themeasuring volume of about 40 μs, whereas according to the prior art 750μs are realized. At the same time it must be said, however, that areduction of the radius of the Gaussian measuring volume by a factor >10is not appropriate since the more than 1000 times smaller dwellingprobability of a molecule in the measuring volume which is reduced bymore than 1000-fold would lead to unacceptably long measuring times.Thus, the optimum of the presented method according to the inventioncorresponds to realized measuring volumes V of from 10⁻¹⁴ to ≧10⁻¹⁷ l.Anyway, with visible light the reduced size of the space element cannotbe further reduced largely due to the diffraction properties of thelight. This could be circumvented, however, by using X-ray radiationaccording to the invention in case nuclear fluorescences are excited inorder to generate measuring signals.

Under the aspects,

-   -   that the measuring times be within a range (ms to sec)        acceptable for practical applications,    -   that the signal-to-noise ratio be significantly >1 and        especially within the range of 100 to 1,000, and    -   that the average times of diffusion of smaller molecules,        molecular complexes, or molecular fragments (through the        measuring volume) do not become too large, lest they be        destroyed by exposition to the radiation designated for        excitation,        an optimum Gaussian measuring volume of ≦10⁻¹⁴ l and especially        ≦10⁻¹⁷ l results.

The signal-to-noise ratio's being quite high is accounted for, inaddition to the fact that the measuring volume is small, preferably byappropriate filters being employed. For convenience, these opticalfilters are interference band filters to suppress Raman scattered lightand/or Raman cut-off filters which “cut off” scattered light closely bythe wavelength of the radiation designated for excitation, with opticaldensities of 10⁻7 corresponding to a suppression factor of 10⁷.

For the method according to the invention and the device forfluorescence spectroscopy of single molecules, molecular complexesand/or molecular fragments according to the invention, it is critical—inaddition to the extremely sharp focusing of the radiation designated forexcitation—that there be a confocally located pinhole aperture having anextremely small orifice in the beam path of the radiation resulting fromexcitation. The size of the orifice of the pinhole aperture in theobject plane is selected depending on the image scale and the size ofthe measuring volume to be imaged in the object plane. With an imagescale of 40 (100) and a radius of the measuring volume of <0.1 μm, aradius of the pinhole aperture of 4 μm (10 μm) will result as a lowerlimit.

Background Scattered Radiation, Especially Raman Radiation

The more intense the exciting laser beam passing through the sample andthe larger the volume element imaged on the single photon detector, theless intense is the radiation scattered by molecules and solids presentin the sample that will reach the detector, that is to say it is moreeasily discriminated from the sought signal by autocorrelation.

According to the invention, a single rhodamin molecule is measured witha signal-to-noise ratio of 1000 in a space element of 0.2 fl, if theRaman band of water is suppressed by conventional filters. Priormeasurements without using such small space elements could realizesignal-to-noise ratios of only 10⁻³.

Life of Fluorescence Dyes Under Light Exposure

The fluorescence dyes which are biologically applicable according to theinvention have only a limited life. Dyes such as fluorescein are evensignificantly more light sensitive. For the precise measurement ofaverage dwelling times, especially of large complexes, however, the dyewill be excited about 10,000 to 1,000,000 times before the molecule willhave left the measuring volume again. Each premature bleachingdeteriorates the measuring result since premature bleaching simulatestoo large a translational coefficient (a smaller molecule).

Diffusion Times of Macromolecular Complexes, Viruses, Cells—ShortMeasuring Times

Particularly large molecular complexes, viruses or cells have extremelysmall translational diffusion coefficients. In the small volumesaccording to the invention, viruses and cells can even be handledwithout significant bleaching of coupled dye labels which have diffusioncoefficients of about 10⁻⁸ cm²/s for free M13 DNA and about 5×10⁻⁹ cm²/sfor an E. coli bacterium. The dwelling time of a bacterium in themeasuring volume is about 30 ms. Larger measuring volumes, which havebeen the only possible ones this far, will result in unacceptably longmeasuring times until those large complexes will have left the measuringelement again through translational diffusion.

Integrity/Preservation of the Complexes Not Present in the VolumeElement

A statistical probability exists, that a dye will react out of theexcited state by some chemical reaction and hence bleach. If thishappens through light from outside the measuring volume, then themeasurement should not be affected since an inactivated dye will notprovide any signal at all and hence would not contribute to themeasurement. However, the quality of the method is drastically limitedby the fact that the effective concentration of measurable molecules andmolecular complexes is decreased by premature bleaching of dye-labeledmolecules which are still outside the measuring volume and hence thesensitivity is affected. Those negative effects will become quitebothersome if the laser beam is not focused to a maximum extent and ifthe label molecule is provided with several dye molecules according to apreferred embodiment of the invention, an undeterminable portion ofwhich has already been bleached by prior light exposure.

Life of Complexes During Measurement

A complex of a target molecule to be detected and a labeled test reagentis detectable according to the invention only in the case that thecomplex remains stable throughout the measuring time. This would not bethe case anymore with average complex dwelling times in large volumeelements in the range of seconds, if the complexes themselves had adecay time in the range of seconds. This can thoroughly be the case withbiologically relevant reactions such as metal ion complexations in whichbinding constants of 10⁶ l·mol⁻¹, for example, are relevant. The smallvolume elements according to the invention, however, mean so shortaverage dwelling times (<1 ms) that for virtually all interestingcomplexation reactions a complex will remain stable throughout itsdwelling time in the measuring volume.

Multiarray Detection

A multiarray detection according to the invention can be performed by alarger volume being illuminated in a non-optimal way with differentvolume elements being imaged separately on a multiarray detector,however, and the incoming photons being recorded and evaluatedseparately during a measurement. This is possible by using multiarraysingle photon detectors as commercially available. One drawback of thismethod is the fact that undesired irradiation will result in significantphotoinactivation outside the measuring volumes. In a multiarraydetection, that is in the parallel FCS analysis of measuring volumes ofdifferent space coordinates or in successive FCS analyses of measuringvolumes of different space coordinates, it is not advantageous, in thesense of what has just been said, that a relatively large volume elementbe illuminated in an experimental array while the measurement of thesmall space elements is performed by simultaneous imaging, measuring andevaluating small space elements arranged in a 2D pattern. In thisexperimental proceeding (FIG. 24), numerous chromophores will bleachalready before having rached the measuring volume by diffusion.

With lower concentrations, accordingly more volume elements will have tobe measured. Since the average measuring time for one measurement rangesbetween 10 and 100 ms depending on the required quality of measured data(signal-to-noise ratio), from 10,000 to 100,000 volume elements can betested in 1000 s. Hence, extremely low concentrations of 10⁻¹⁴ to 10⁻¹⁵M can be measured. This also means that specific biological interactionswith binding constants k_(ass)≧10⁶ mol/l up to k_(ass)=10¹⁵ mol/l can bemeasured.

One example demonstrates how binding constants or reaction rateconstants may be measured using the technique according to theinvention. The measurement of a binding equilibrium between reactantsaccording to the invention is based on the fact that at least onereactant is preferably chemically coupled to at least one dye moleculeand the rotational diffusion rate and/or the translational diffusionrate of the reactant will change during complex formation. Ifequilibrium constants are not directly compatible with the experimentalcondition of highly diluted solutions, that is to say, if low bindingconstants require higher reactant concentrations, this can be achieved,for example, by offering an excess of the non-labeled reactant or byadding an excess of unlabeled reactant to the labeled compound.

The measurement of reaction kinetics through molecular fluctuation usingFCS, as has been described by Magne, could not be carried outsatisfactorily in the measuring compartments realized this far due tothe long diffusion paths. With the measuring technique according to theinvention, the determination of the dissociation rate constant of acomplex is possible in a range of from 10⁻⁶ s⁻¹ up to about 10³ s⁻¹,which range is particularly relevant for biochemical reactions. Suchmeasurement can be performed, for instance, by interchange offluorescence labeled label molecules.

The technique according to the invention also allows for the measurementof conformational changes in biological macromolecules as well as thedetermination of related thermodynamic and kinetic constants.Fluctuations of the structure can be detected, for instance, throughmeasurement of rotational diffusion or through signal changes byso-called energy transfer (Forster transfer).

This method is applicable in DNA/RNA analysis as well (DNA/RNA analysis,see below). In genetic analysis, particularly for the determination ofinfective pathogens, the sensitivity of the diagnostic method is oftencritical. This has become evident especially in recent years inconnection with the introduction of enzyme-based methods for theamplification of genetic target sequences. It can be expected that byemploying this method the necessity of a preliminary enzyme-basedamplification can be avoided for several diagnostic methods, wherebyproblems of contamination with strongly amplified single sequences canbe circumvented, for example.

The method can also be used instead of the known diagnostic methods ofRIA, ELISA or other methods (see below, receptor screening). Oneparticular advantage of the method according to the invention may beseen in the fact that the system is self-calibrating. Establishments ofcalibration curves or internal standardization need not to be done. Eachexperiment obtains its internal calibration from the determination ofthe molecules considered. For instance, variations of laser intensitywill not affect the accuracy of measurement. A problem of drifting withsuccessive measurements does not emerge. Measurements can be repeated atdifferent times without renewed calibration yielding the same results.Calibration of the devices can be omitted.

One preferred application are assays without participation of antibodiesas test reagents or for substitution in conventional assay methods whichhave been based on ELISA, RIA or FIA using antibodies. Considered areall assays employing other molecules in addition to antibodies asspecifically recognizing molecules (receptor molecules, test reagents)in order to recognize particular target molecules (ligands). In general,possible receptor molecules, in addition to antibodies, are allmolecules or molecular complexes which have specific recognition siteson their surfaces (e.g. antibodies, single-strand antibodies, membranereceptors, soluble receptors, enzymes, structural proteins,polysaccharides, peptides, complex secondary metabolites, etc.) orcontain specific recognition sites for target molecules inside (e.g.HDL, VLDL, LDL).

If the formation of a specific complex between a receptor and one ormore ligands in the general form is of analytical interest and/or if atleast one of the involved molecules can be provided with at least onedye label and the complex formation becomes evident through change ofrotational diffusion- and/or translational diffusion of the dye label,then an FCS assay can be performed. Similar thermodynamic regularitieswith respect to an advantageous embodiment will apply thereto as applyto the corresponding assays of the ELISA, EIA, RIA or FIA types (seeFIGS. 1, 2).

The performance of the method according to the invention becomes evidentin particular when compared to technologies presently being in themarket. A well introduced method is the so-called FPIA technology ofABBOTT, Chicago, using the so-called TDX system for the relatedinstruments. Here, the depolarization of fluorescence labeled moleculesis determined in homogeneous assays.

Depolarization of the emitted light of a fluorescence dye followingexcitation with polarized light is a property, which primarily dependson the molecular weight of the molecule an its shape parameters. Arelatively small molecule will rotate more frequently within the periodbetween excitation and emission of the fluorescent light than asignificantly larger molecule would which results in a correspondinglystronger depolarization of the emitted light. This effect is made use ofas small fluorescence labeled molecules compete with unlabeled targetmolecules for e.g. antibody binding sites. Fluorescence depolarizationwill then provide information about the relative portion of the labeledmolecules bound in the complex. However, this method evidently does notreach the desired detection limits. The manufacturer herself gives alower detection sensitivity of 10⁻⁹ M. The method according to theinvention is more sensitive than this by more than two orders ofmagnitude even without optimization. This is true when the FPIA kits areused according to the invention. By using more sensitive dyes,additional orders of magnitude of increased sensitivity may still beattained. This is very important e.g. in drug diagnostics.

The method according to the invention exhibits its superiorityparticularly in a quantified assay and in quality depending on varyingsample conditions. The degree of fluorescence depolarization depends onthe conditions viscosity/temperature of the medium. With increasingviscosity, the degree of fluorescence depolarization of all moleculesdecreases due to lower rotational diffusion coefficients and immediatelyaffects the results. Similarly interfering effects can be causedconditions of the medium affecting the life of the excited state.Prolonged life will simulate an increased fluorescence depolarization.In the method of measuring the translational diffusion according to theinvention, however, those effects do not adversely affect the quality ofthe results. In practice, this means a significantly smaller expenditurein sample preparation and scaling of the method and a notably largerrange of dynamic measuring width.

2. The Significance of Reaction Rate for Complex Formation

As in the case of nucleic acid reassociation (see below), with otherspecific recognition reactions the association rate can also be so slowthat a homogeneous assay based on this recognition reaction ist notpracticable. Whereas in inhomogeneous assays reactants are often offeredin excess, for instance when working with labeled antibodies, in orderto increase the reaction rate of the specific complex formation and theexcess of reactants not bound to the complex is removed in a subsequentstep, this cannot easily be done in homogeneous assays.

This problem shall be illustrated by means of an example: The detectionaccording to the invention allows for the determination ofconcentrations of compounds labeled with fluorescent dye in the range of≦10⁻¹⁵ M. If a fluorescence labeled specific test reagent is employedfor a target molecule or a molecular complex, at least threerequirements must be met: 1. The difference in size between thefluorescence labeled molecule not bound to the complex and boundfluorescence labeled molecule must be larger by a factor of about 2 interms of diffusion constant in order to be readily detectable throughthe different translational diffusions; 2. the binding constant must besufficiently large to complex the target molecule, 3. the reaction rateof the association must be sufficiently large to realize complexformation within an experimentally acceptable period of time rangingfrom minutes up to hours at most.

If one complexed target molecule among 100 molecules of the test reagentnot bound to the complex can be detected, then according to theinvention a concentration of 10⁻¹³ M of test reagent can be employed todetect a formed complex of 10⁻¹⁵ M. In the equilibrium, complexformation can take place efficiently, if the corresponding associationconstant k_(ass) for the bimolecular reaction is at least 10¹³ M⁻¹. Suchhigh binding constants will occur only rarely with biological moleculessuch as proteins.

The binding constants of antibodies usually are in the range of 10⁶ to10¹⁰ M⁻¹.

The reaction rate constants of antibodies for the bimolecularcomplexation reaction hardly exceed the range of k_(ass)=10⁷ M⁻¹s⁻¹. Thedifference in the binding constants principally results from thedifferences in dissociation rate constants k_(diss) of the complexeswhich often range between 10 and 10⁻³ s⁻¹. For the case discussed above,however, a rate constant of K_(ass)=10⁷ Mol⁻¹s⁻¹ means that the halflife of association would be around 1000 s already if concentrations of10⁻10 M of test reagent were employed.

According to the invention, several alternatives arise to make use ofthe sensitivity of the optical detection reaction, being 10⁻¹⁵ M for ahomogeneous assay, for the recognition reaction despite of lower bindingconstants.

The effective association rate can often be changed dramatically byalteration of the reaction conditions. For nucleic acids it is describedbelow how the association of complementary nucleic acid sequences can beaccelerated by 10,000 to 100,000 times. Recognition reactions ofsequence motifs on long-stranded DNA proceed faster than could beachieved by pure diffusion control. Probably, the rate-determining stepis the arrival of the protein factor at the DNA followed by a fastone-dimensional diffusion step along the DNA to the actual site ofbinding.

An acceleration can in general be achieved by shortening the diffusionpathways of the rate-determining step of association. This is done, in arather trivial way, by concentrating the reaction mixture.

According to the invention, the conditions of the medium are varied inthe homogeneous assay such that the effective dwelling space of thereacting molecules is reduced without reducing the sample volume assuch. According to the invention, this can be done, for instance, byadditives such as poly(ethylene glycol)s, dextrane, polyvinylpyrrolidon,chaotropic reagents, organic solvents or combinations thereof whichprimarily affect the structure of the hydrate water coats. According tothe invention, aqueous two-phase systems may also be used to enrich thereactants selectively in one of the phases.

Another possibility is the use of excess components of the labeledreactant. If two dye-labeled reactants are used, which can recognize andbind one analyte jointly, so-called energy transfer complexes can beformed. One dye label serves as an acceptor of the exciting light whoseemitted fluorescence light will excite the closely neighboring seconddye molecule (10-100 Å) which will then emit light detected as themeasuring signal according to the invention. Because the efficiency ofenergy transfer decreases with the sixth power of the dyes' distance,the reactants can be used in excess. The translational diffusioncoefficient of the ternary complex is measured according to theinvention.

The use of the dye-labeled test reagent as an excess component is alsopossible according to the invention, if the uncomplexed test reagent canbe modified chemically or by irradiation with respect to itsspectroscopic properties such that it becomes spectroscopically distinctfrom the complex. This is possible, for instance, in the case ofintercalating dyes.

The concentration by means of an electric trap according to theinvention is described somewhere else in the specification.

If complex formation only weakly contributes to a change in molecularweight and/or shape of a test reagent, such as, for instance, in the useof a labeled antibody against a small ligand, then the use of a secondantibody in excess which is directed against the complex according tothe invention can render the produced ternary complex detectableaccording to the invention.

According to the invention, at least two different test reagents with atleast two different dye labels, which are able to react with at leastone target molecule wherein the fluorescence signals of at least twodyes are measured according to the invention, can also be used. Thismethod can be employed in two ways.

a) Parallel determination of at least two different analytes in asample.

The experimental problem frequently arises to detect several analytestogether in one sample. Instead of two independant assays, detection ofat least two different analytes can also be performed independentlyaccording to the invention by reaction of two independant test reagentswhich are labeled with at least two independant and different dyes andpreferably can either be excited with light of different wavelengths orindependantly detected by light of different emitted wavelengths. Thiscan be achieved, for example, by using two independant optical systemssuch as those schematically outlined e.g. in FIG. 16.

3. Cross Correlation

b) Increasing detection specificity by simultaneous binding of at leasttwo test reagents to one analyte.

Some analytes can be differentiated only with unsatisfying specificityfrom similar analyte molecules by binding one test reagent. These may beexemplified by homologous nucleic acid sequences which can bedramatically different with respect to their biological activities, suchas e.g. their own pathogenicity or the pathogenicity of their products.Proteins, such as tumor antigens, structural proteins, or cell-typespecific surface markers, can also be analyzed but unsatisfactorily bybinding just one ligand.

According to the invention, a particular molecule can be complexedsimultaneously with at least two test reagents which are labeled eachwith at least two optically distinctive fluorescent molecules. Accordingto the invention, the simultaneous complex formation can be detectedeither specifically through formation of an energy transfer complex(Förster transfer, see above) or through correlation of the signals ofexcitation and/or emission having different wavelengths. Binding ofdifferent test reagents to one analyte is proven by time correlation ofthe distinct optical signals.

The double complexing of an analyte with two differently labeled testreagents not only has the advantage of increased specificity, asdiscussed above, but also the practical advantage that higherconcentrations of each individual reagent can be used. By means of timecross correlation of the fluorescence signals detected according to theinvention, the signals of the uncorrelated free test reagents can beefficiently suppressed at the level of electronic signal processing.This method can be used especially well with nucleic acid analytes byemploying at least two differently labeled test reagents which will bindto different sequence segments of the analyte. The emitted wavelengthsof the respective fluorescences of the different dyes are distinct.Instead of the sole autocorrelation of the detected signals, which isotherwise usually measured, cross correlation of the signals ofdifferent wavelengths is measured according to the invention. If bothprobes are simultaneously bound to the target analyte, then crosscorrelation will yield the number of molecules and the diffusion time ofthe doubly labeled nucleic acid segment. Probe molecules which are notbound are visible in autocorrelation, whereas their signals aresuppressed in cross correlation.

4. Method and Device for Performing Fluorescence Correlation Microscopy

Thus, cross correlation of fluorescence signals of different dyeschemically linked or physically associated with a molecule or molecularcomplex can be used to increase sensitivity and enhance specificityaccording to the invention. To perform the experiments in an optimumway, however, several requirements must be met which can be achieved toparticular advantage by the method according to the invention presentedherein in the following as well as by a related device.

The method according to the invention pertains to the combination of themethod of cross correlation with fluorescence correlation spectroscopyusing small measuring volume elements. This method must be clearlydifferentiated from such correlation methods as employed e.g. in FACSanalysis (fluorescence activated cell sorting). Several opticalparameters derived from a large complex such as a cell are also measuredsimultaneously therein, e.g. the forward light scattering in combinationwith a fluorescence signal or the simultaneous measurement of distinctfluorescence signals. In the cell sorter, the signals of single dropletsare measured in which single cells may be present. Therein, bycorrelation of signals to identify cell types and subtypes is only meantthe intensity distribution of different signals which is detectedintegrally throughout the droplet. Correlation is considered thereinonly to mean the parallel detection of several parameters with respectto their individual intensity. The method described herein time-linkstwo stochastic processes, the diffusion characteristics of differentchromophores in a small space element. On the level of a cell, thismeans virtually that the method according to the invention is able todistinguish between different molecules bearing a chromophore and beingpresent in the measuring volume whereas in the cell sorter, theconcentration of this chromophore is determined integrally in thedroplet, irrespective of whether it is part of a small molecule or itoccurs in a complex or bound to a cell.

Cross correlation in connection with FCS analysis is intended to meanthe following methodology: A volume element is illuminated by a laserbeam or X-ray beam which is as strongly focused as possible. Theintensity of the electromagnetic radiation is chosen so high that alarge percentage of molecules that can be excited by the radiation existin the excited state. The fluorescent light emitted by them is detectedby confocal imaging by means of a pinhole aperture in a single photonmeasuring device so that only a small volume element of the elongatedcone of light is measured. When a molecule migrates into said volumeelement by diffusion, it is excited and measured through the emittedlight as long as it remains inside this measuring volume element. Theaverage dwelling time is characteristic for the size and shape of amolecule, a molecular complex, or a cell.

In this way, molecules being present at different concentrations can bedistinguished or simultaneously counted by correlation spectroscopy. Forinstance, binding constants for complex formations of e.g.receptor/ligand interactions or kinetic constants such as decay rates ofsuch complexes can be determined in this way. The method will yieldoptimum results if particularly few molecules with fluorescentproperties are present in the volume element per unit of time. This isthe case for concentrations in the range of 10⁻⁹ and below. Conversely,however, the problem arises that complex formation with a secondreactant will not proceed any faster than by 10⁷/s. For equimolarconcentrations for two reactants of 10⁻⁹ M, this means a reaction timeof more than one minute. Shortening of the reaction time can beachieved, for instance, by using an excess of the fluorescence labeledreactant. With a reactant concentration of 10⁻⁹ M, complexes with targetmolecules with a concentration of 10⁻¹² M can be detected in this wayafter minutes of reaction time. With lower concentrations, thesignal-to-signal ratios of complex and free ligand become too high toallow for reliable concentration measurements. Another experimentalproblem arises if the binding constant of a complex to be measured isnot high enough to employ ligand concentrations of ≦10⁻⁹. Virusantigens, nucleic acids of pathogens, or certain hormones, however, haveto be detected in concentrations which are significantly smaller than10⁻⁹ M. A typical application field is the diagnostics of tumor antigensthrough monoclonal antibodies which often have a low binding constant aswell as not too high a specificity in distinguishing the tumor antigensof a dedifferentiated cell from the antigens of the respectivedifferentiated cell. Cross correlation using two different chromophoresallows to increase sensitivity and specificity in the sense discussedabove.

At least three chromophore bearing molecules or molecular complexes needto be distinguished experimentally: free ligand with chromophore 1, freeligand with chromophore 2, complex with chromophore 1, complex withchromophore 2, and complex with chromophore 1 and chromophore 2. Only acomplex bearing both chromophore 1 and chromophore 2 throughout theperiod during which the complex is present within the measuring volumeis indicative of a target molecule to be detected such as a tumorantigen or a pathogen, such as a virus, or a related DNA or RNA.

Now, in cross correlation the signals of chromophore 1 and chromophore 2are correlated. Only in the case that a molecular complex is excited inwhich in one and the same window of time, wherein the molecular complexis present within the measuring volume, both types of chromophore aredetected, these signals are assigned to a complex bearing bothchromophores.

Critical requirements for a successful cross correlation are:

-   -   The distance between chromophores 1 and 2 on the target molecule        must be small compared with the dimensions of the measuring        volume, so that both dyes are hit by the exciting light        simultaneously within the error limits of the measurement, when        they enter the measuring volume and leave it again (distance in        the complex <0.1 μm).    -   The measuring volume must have the same dimensions for both        dyes, so that both dyes, when linked to one another, are in        contact with the respective exciting light within an identical        window of time.    -   Both measuring volumes must have the same space coordinates        within the error limits of measurement.

Solving this problem is in no way trivial. For instance, one problem isthe fact that light of different wavelengths will result in differentimage sizes due to different refractive indices, as is well known. Itwould be disastrous to the measurement, however, if two lasers withdifferent wavelengths illuminated unequally sized volume elements due tounequal focusing, or if detecting on the photo multiplier covereddifferent measuring volumes.

According to the invention, this problem is solved either by using onlyone laser with one exciting wavelength in connection with the use of twodyes with strongly overlapping exciting spectra which can bedistinguished, however, by the so-called Stoke shifts of at least twoemitted wavelengths. Alternatively, volume elements having identicalspace coordinates are illuminated by two independant laser lightsources. For convenience, the optics of confocal imaging is colorcompensated in both cases, i.e. corrected for both emitted wavelengths,so that one and the same space element is measured for both wavelengths.

According to the invention, imaging optics which is conventional inmicroscopy is used for imaging the fluorescent light of differentwavelengths which will image light of different wavelengths withidentical scaling. For the performance of the method according to theinvention it is also critical, however, that space elements of identicalsize, identical intensity profile, and identical space coordinates beilluminated for both wavelengths. This is achieved by using, accordingto the invention, a device on the side of excitation optics in whichboth laser beams are prefocused before entering the sample whereineither two fixedly adjusted optics having different magnification valuesare employed so that, as a result, both wavelengths are prefocused withthe same dimensions and geometry of the beam, or else a device withfixedly adjusted prefocusing optics is used, that is in combination witha variable beam expander for the second beam path or by employingvariably adjustable beam expanders for prefocusing in both beam paths.

For convenience, the device is realized as a compact double microscopewhose two objective lens arrays, oriented to two opposing sides of themeasuring compartment to be illuminated, can be shifted along theiroptical axes. The optics for the incident light beams and for the lightbeams emitted by the molecules, molecular complexes, vesicles, or cellsof the measuring compartment are arranged on two sides of a commonguiding or supporting device for each “moiety” of the double microscope.Each of the incoming light beams are deflected towards the objectivelenses by dichroic mirrors. The returning light beams penetrate thesedichroic mirrors rectilinearly to hit a detector after having passeddiverse optical elements, such as lenses, confocal elements, and filterdevices.

For convenience, the optical axis of the light beams impinging on thedichroic mirrors is oriented perpendicular to the shifting direction ofthe two objective lenses. The two light beams of different wavelengths,superimposed, impinge on mirrors located one behind the other, the firstof which in the beam path is a dichroic mirror. One of the two lightbeams is deflected by this dichroic mirror whereas the otherrectilinearly penetrates this dichroic mirror to be deflected by thereflecting mirror behind in the direction opposite to that of the firstlight beam. The deflection directions of both light beams are parallelto the shifting direction of the objective lenses. The deflected lightbeams are again deflected by reflecting or dichroic mirrors to passthrough the optics for the incoming light beams. This arrangement of theoptical elements of the double microscope has the advantage that the twoobjective lenses along with the optics for the light impinging on themeasuring compartment and proceeding therefrom can be displaced withoutthe need to displace or shift the light generation sources along withthem. The light generation sources which are, in particular, lasersources, can be positioned remote from the double microscope; only therelative position between the light generation sources and the site ofthe double microscope where the two light beams are superimposed and fedin must not change.

The device can also be employed in the case when it is necessary tocover fluorescence signals from the measuring volume over the total 4πsolid angle. In particular, this may be the case when it is critical tocover all emitted photons in the detection of one single molecule. Inthis case the device described would be used in such a way that only oneexciting wavelength is employed and both detecting optics together coverthe total 4π solid angle.

FIG. 1 illustrates a receptor assay for related effector molecules usingreceptor bearing cells wherein the receptors have specific bindingproperties as to a ligand L. The ligand is provided with a dye labelaccording to the invention. According to the invention, the molar ratioand the total concentrations of receptors and ligand are selected toadvantage such that about 50% of the receptors are occupied and about50% of the ligands remain unbound. In the analysis according to theinvention, this can be seen by the fact that about the same number ofemitted light signals are detected from molecules with fasttranslational diffusion as are detected from molecules with slowtranslational diffusion (schematic drawing on the upper right; the stepon the left corresponds to the free ligand, the step on the rightcorresponds to the receptor bound ligand)

When a potential active substance is added, a shift of the equilibriumindicates interaction of the candidate active substance with thespecific receptor binding. In the case of an antagonistic activator orblocker of the receptor function, displacement of the labeled ligandwill be observed (the signal only corresponds to that of the freeligand). The same signal can be obtained if an allosteric interaction ofthe active substance with the receptor or with the ligand preventsbinding of the labeled ligand.

In an analogous way, a potential active substance can also enhancebinding of a ligand to the receptor so that measurement of bound ligandwill be increased (lower right).

The assay can also be performed in the case that the cell bears morereceptors which do not interfere with the specific reaction observed.

If the equilibrium in a receptor recognition reaction is not quicklyreached, it may be of advantage to make the labeled ligand and thepotential active substance compete for the receptor simultaneously.

FIG. 2 describes the use of potentially different receptors on differentcells which, however, will possibly recognize a defined natural ligandwith the same specificity and binding strength, but will transmitdifferent signals. Potential active substances could be of interest toselectively activate or block those receptors. This can be achieved withmutants/variants of the natural active substance as well as with activesubstances which are not structurally related.

For instance, the assays for the respective target receptors are firstperformed separately. Here, the rules which are given in the legend ofFIG. 1 will apply. A potential active substance is primarily assayed forinteracting effectively and specifically with one of the studiedreceptor bindings and thus for allowing to separate different receptorfunctions (possible cases on the lower left). With effects acting in thesame direction, measuring results such as shown on the lower right canbe found.

As will be set forth in more detail below by means of specific examples,FCS assays according to the invention are especially, prominent becausethey are not limited to antibody mediated specificity, are equallyuseful for molecular, cellular, tissular systems in homogeneous or insolid phaseLassays, allow for the determination of thermodynamicparameters (binding constants) and kinetic parameters (rate constants),allow for nondestructive investigations of living systems (cellcultures, tissue), and unspecific interactions with surfaces do notinterfere when analysis takes place in solution.

5. Screening of Pharmacologically Active Substances Through Binding ofKnown Fluorescence Labeled Ligands to Unknown Receptors Which May bePresent on Cells or on Natural or Artificial Vesicle Structures

Natural as well as chemically synthesized pharmacologically activesubstances exist the target molecules of which are not known. Thosetarget molecules may be extracellular molecules (e.g. proteaseinhibitors), surface membrane receptors (e.g. insulin), soluble mediatorreceptors (steroid hormone binding receptors), or cellular structuralproteins, or enzymes.

Hence, according to the invention the extremely important problem can besolved to find, characterize and optionally to isolate thepharmacologically important target molecule of a known active substance:

-   -   search for orphan receptors    -   revelation of the mechanisms of pharmacological action    -   search for analogous active substances    -   search for and distinction between different receptor molecules,        preferably in distinguishable biological targets (different cell        differentiation, tumor/non-tumor, pathological/non-pathological,        etc.).        Pharmacokinetics

According to the invention, pharmacokinetic investigations may also beperformed:

-   -   after different intervals of time following administration of a        particular active substance, tissue samples or body fluids can        be analyzed in competitive experiments using freshly added        dye-labeled comparative substance.        Distinguishing Between Target Molecules of Active Substances        Through the Dissociation Rate Constant of the Complex

If an excess of dye-labeled active substance is added to a mixture ofdifferent complexes between receptors and the active substance, thennearly each dissociated molecule of the active substance will bereplaced by dye-labeled active substance. Optionally, the experiment maybe carried out with reverse labeling as well. For example, a typicalproblem is the analysis of different cell lines in order to detectdistinct receptors (example: tumor surface antigens, protein P bindingreceptors type I, II, III). Typically, a diagram such as that depictedin FIG. 19 will be found, if many samples are analyzed simultaneously.According to the invention, large amounts of analyses are analyzed in anexperiment simultaneously and/or repeatedly over a long period of time,when dissociation rate constants are slow, by analyzing thedetermination of the ratio of initially bound and dissociated activesubstance iteratively in all positions after fixed intervals. FIG. 19contains a schematic drawing of the results.

In this way, different receptors or antigenic determinants may beassayed, for example, which form complexes of different thermodynamicstability with a specific target molecule in one and the same sample orin different samples with e.g. different cell types or differentiationstages, whose dissociation rates (k_(D)) are drastically different whiletheir reaction rates values (k_(R)) are often comparable. Thus,biological guiding structures for so-called orphan drugs or orphanreceptors or members of multifunctional molecular families can bedetected by means of functional assays.

In practice, advantages in handling especially arise from the fact thatworking in homogeneous solution allows for very short incubation timesfor routine analyses in the nM range which are virtually no longerrelevant (range of seconds to minutes), and there are no extensivewashing steps or secondary incubations.

As sample carriers, sheet-like carrier systems are preferably used whichmake it possible, according to the invention, to approach the liquidsample close to the objective without contact and hence withoutcontaminations (FIG. 3).

FIG. 3 illustrates the use of carrier sheets having wells thereon suchas described or used, for instance, in the patent applications PCT/EP89/01320, PCT/EP 89/01387, PCT/DE 91/00082, PCT/DE 91/00081, PCT/DE91/00083, PCT/DE 91/00704. The reaction carriers, referred to asmulti-well sheets, bear wells which can receive the samples for FCSanalysis according to the invention. They are controlled by atwo-dimensionally positionable sheet insertion device such that thebottom of the sample containing well is approached closely to theobjective, so that the liquid sample volume is not further away from theedge of the objective than about 100-1000 μm. H₂O is the preferredmedium between sheet and objective, to which the correction of theobjective is preferably related (see above). The sheet is opticallyclear and chemically inert with respect to both the exciting light ofthe laser and the emitted light. In a preferred procedure, the sheetsare sealed by a cover sheet. Sheets are preferred which have a distancebetween wells corresponding to the commercial microtitration format orOkasaki format, since automatic pipetting devices for those formats areavailable in the market in great numbers. Moreover, sheets as reactioncarriers are low-polluting, easily disposed and can be filedspace-savingly in the sealed state.

6. Analysis of Ionic Molecules

Charged molecules (cations and anions) can be analyzed specificallywithin the measuring compartment of the method according to theinvention by employing an “electric trap”. This can be done, forinstance, by inducing a molecular flux through the measuring compartmentwherein, with or without superimposing by a mechanically induced flux,an electric field causes concentration of particular ionic molecules inthe observation compartment or a single molecule is transported into thecompartment directedly. This can be achieved by a rectified field, e.g.between the outlet ends of two capillaries with a fiel strength in therange of about 1 V/1 μm. According to the invention, it can also beaccomplished to make one or more trapped molecules oscillate in analternating electrical field in the observation compartment as soon asthey have entered this volume element (see below).

Technical Description of the Device According to the Invention

7. Optics

The method according to the invention can be performed technically withmicroscope optics of high quality with respect to the image quality ofthe focus. In particular, the lens system before the emergence of theexciting light must be chromatically and spherically corrected.Preferably the system Neofluar of the company Zeiss, Oberkochen, Germanyhaving a high numerical aperture ≧1.2 N.A. is used with or without coverglass or separating coat. The operating distance is 0.17-0.9 mm. Theobjective is corrected for water and offers maximum numerical aperturewith maximum operation distance. Oil immersion objectives are lesssuitable. According to the invention, the light quantity is limited by aconfocal pinhole aperture in the object plane behind the microscopeobjective.

8. Laser Light Source

As laser light sources for wavelengths of >200-1000 nm continuous lasersare preferably employed, especially lasers of the argon, krypton,helium-neon, helium-cadmium types as well as tunable diode lasers (redto infrared regions), each with the possibility of frequency doubling.According to the invention, the use of pulsed high frequency lasers of≧10 MHz is also possible.

9. Laser Intensity

A laser intensity of 0.5 mW is already sufficiently high that a fewpercent of the dye molecules in the observation volume are excited. Witha laser intensity of 5 mW, the percentage of excited molecules isalready 50%. Thus, further increase of the laser power does not appearappropriate for increasing the light efficiency.

10. The Luminophore

Possible luminophores or fluorescent dyes apt to be coupled are a greatnumber of fundamental dye structures as well as oligomers of those dyesas employed for a long time in fluorescence spectroscopic detectingmethods. Preferred dyes are those which either do not themselvescontribute to specific, interfering interactions with target moleculesor are employed specifically making use of specific binding propertiessuch as being capable of nucleic acid double-strand intercalation, ashas been proposed in P 42 34 086.1 (Henco et al.).

Preferably, the dyes employed have an absorption coefficient betweenabout 30,000 and 100,000 with a quantum yield of 0.1-1.

For example, dyes from the coumarin series, or rhodamine B derivativeswith a high content of hydrophilic residues to prevent hydrophobicinteractions, or dyes based on thiazole orange fundamental structureswhich are capable of intercalating in double-strands have proven to besuitable.

For the measuring method according to the invention, resistance of thedyes to photobleaching (bleaching stability) is an important property.However, as has been mentioned earlier, it is no longer of outstandingimportance for the performance of the measurement since measuring timeshave shortened by some orders of magnitude as compared with measuringcompartments which are about 1000 times larger when very small measuringvolumes according to the invention are employed.

11. Significance of the Triplet State

According to the invention, dyes are preferred which do not tend to formtriplet states.

When selecting dyes, it is of great importance to select those dyeswhich have a very low tendency to form triplet states. Each tripletstate entered raises the probability of a chemical reaction, does notprovide a signal or provides a signal with an undesired wavelength, andextends the period until the molecule is ready to be excited into thesinglet state again.

If dye multimers are employed for labeling, particularly those based onhydrophilic dyes such as certain coumarin derivatives, then measuringtime can be shortened significantly. The larger number of individualmeasuring values has the result that less events of molecular passagethrough the measuring element must be pursued to obtain sufficientmeasuring accuracy.

12. Measuring Compartments

According to FIG. 4, the measuring compartments must be approached tothe emergence objective of the laser-focusing optics at 100-1000 μm. Inthe simplest case, this is done by means of a drop hanging on theobjective itself and containing the molecules to be analyzed. Such ameasuring set-up can be used only for a few analyses since the risk ofcontamination between different samples is high. Techniques comparableto those of conventional microscopy with cover glass and oil immersioncan be employed. The method according to the invention uses waterimmersion and very thin glass or plastics sheets to separate the aqueoussample from the optics. The sheets can at the same time serve to sealthe compartments underneath in the form of flat carriers or in the formof capillaries.

For the application of screening large numbers of samples, as occur inexperiments with evolutive optimization of biopolymers, membranes arealso used which are chemically modified on the side directed to thesample. Preferred modifications are surface structures having specificbinding properties, such as e.g. ion-exchange properties to fix nucleicacids, and/or specific binding properties with respect to proteins, suchas antibody coating or coating with chelating agents, especially NTA(nitrilotriacetic acid) or IDA (iminodiacetic acid), to selectively fixrecombinant proteins or peptides with binding oligopeptides, such as(His)₆, which can be bound to surfaces through metal chelates with highbinding constants (k_(ass)≧10¹⁰) in order to analyze them for theirrespective properties of interaction with target structures.

13. Molecular Trap

Another possibility for the described detection of single molecules insmall volume elements is the use, according to the invention, of amolecular trap using an electric field, which shall be described later.This kind of analysis can be applied, however, only to molecules apt tointeract with the electrical field, such as ionized molecules.

14. Detection

Detection of the measuring signals preferably takes place through theoptics of a fluorescence microscope with single photon counting whereinan avalanche diode detector is preferably used. For instance, the use ofSPC-100 and SPC-200 of the manufacturer EG & G has proven to beappropriate. Signal analysis is performed with a digital correlator or amultichannel counter MCS.

Method and Application

15. Characterization of Molecules

The correlation method directly reveals three characteristic molecularquantities: the number (N), the translational diffusion coefficientD_(t), and the rotational diffusion coefficient D_(r). The latter twoare a function of molecular size and shape (i.e. radius, shape andvolumej and provide information about changes of the molecule, e.g. byenzyme cleaving or complexation with other ligands, etc. Becausemeasurement of diffusion correlated diffusion times can be performedquickly and with high sensitivity according to the invention, the methodfor analyzing molecular sizes and their distribution in a population insolution can be used without the need of chromatographic separation.

16. Determination of Binding Constants

As R. Rigler has shown, analysis of the correlation function formolecules reacting with one another has the result that the interactioncan be determined my measuring the number of molecules N and theweighting factors of the characteristic diffusion times. In the casethat the value of the reaction rate constant is slower than diffusiontime, which always will be the case in specific reactions, thecorrelation function is given as the sum of the weighted diffusiontimes:G(t)=1+1/N(x(1+t/τ _(x))⁻¹ +y(1+t/τ _(y))⁻¹)where x, y, and τ_(x), τ_(y) are the proportions and diffusion times ofmolecules X and Y. τ=ω²/D. ω is the radius of the sample volume and D isthe diffusion constant.

In the case that reaction rate constants are faster than diffusiontimes, the correlation function becomesG(T)=1+1/N(1+4<D>t/ω ²)⁻¹where <D>=xD _(x) +yD _(y).

If D_(x) and D_(y) are different, the binding of a (small) ligand to alarge target molecule as the receptor (protein, nucleic acid, antibody)can be followed in a simple way without molecular separation processesthat are usual in so-called inhomogeneous assays. Correspondingrelationships can also be deduced for the rotational diffusioncoefficients or rotational diffusion times. The high measuringsensitivity exceeds that of radioisotope methods as known from theradioimmunoassay techniques (RIA) These are equally good only whenlabeling with high specific radioactivity. When performed according tothe invention, molecular separation processes and time-consumingcalibration can be omitted. Hence, the correlation method represents analternative to the radioimmunoassay used today. According to thetechnique described above, a fluorescence labeled antigen whose bindingto an antibody is analyzed in competition with the antigen to bedetermined in homogeneous phase or inhomogeneous phase (solid phasecoupled) is employed instead of the radiolabeled antigen reagent. Oneadvantage of the method according to the invention is based on the factthat undesirable radioactivity can be omitted while at the same timeincreasing the sensitivity of the measuring method.

17. Products of Enzyme Reactions

Where enzyme catalysis results in a change of molecular structure andmolecular weight, the formation of reaction products can be followedthrough the change of the number of molecules and of diffusion times.Typical applications are replication and cleavage of nucleic acids,cleavage of proteins and peptides, but also selection of catalyticantibodies.

18. Molecular Dynamics in Membranes and Cells

The possibility to measure the rotational diffusion of large moleculesin viscous environment using the FCS method is of particular importancefor the analysis of the dynamics of specific receptors on cell surfaces,but also inside the cell. At the same time, binding of labeled ligandscan be measured by measuring rotational diffusion and translationaldiffusion at cellular structures, such as receptors etc. Examples areneurotransmitters, tissue factors, such as growth hormones, but alsocationic ligands such as Ca²⁺.

The method according to the invention can also be performed involvingmolecules that do not fluctuate or fluctuate very slowly. This is thecase, for example, if measurement takes place in highly viscous media,in gel matrices or tissues, using solid phases or with very largemolecular complexes or cells involved.

Surprisingly, even cells can be measured in aqueous suspension despiteof their large masses. Brownian motion and turbulences are sufficientlyhigh to move e.g. a membrane segment with its receptors into themeasuring volume and out again without intervening bleaching phenomenaof the dye labels occurring. Schematic FIG. 5 depicts the measurement ofnearly stationary molecules according to the invention. As indicated bythe rectangle, for instance, they may be present as membrane receptorson an immobilized cell (rectangle). The coordinate axes illustrate theanalysis, according to the invention, of non-fluctuating molecules aswell by forced relative motion of the measuring volume with respect tothe stationary element. This can be done by a relative change of thelaser coordinates, of the coordinates of the measuring volume, or of thecoordinates of the sample volume, or of a combination thereof.

When fluctuation is strongly limited or the dye labels are bound in astationary way, fluctuation with respect to the measuring volume must beforced according to the invention. This is achieved by forced motion ofthe sample volume and the measuring volume contained therein (e.g.vibration, flow) and/or continuous or discontinuous change of thepositional coordinates of the measuring volume within the sample volume.This is preferably done by changing the focus and/or by changing theposition of the illuminated volume element. In the special case of afixed label molecule, the relative motion with respect to the positionalcoordinates of the measuring element thus forced exclusively determinesthe “apparent” translational diffusion of the bound dye. To achievediscrimination of dye molecules which are coupled to non-fixedmolecules, the forced relative motion must be slower than that of thenon-fixed molecules.

The procedure described according to the invention is possible in thecase that the time of translational diffusion of the slowly diffusingcomplex is irrelevant for analysis and rather the absolute or relativenumber of the dye labels linked thereto is of interest. This is thecase, for instance, in determining receptor binding constants on cellcultures or in tissues.

The method according to the invention allows for the measurement ofmolecular and/or cellular mobilities in an especially advantageous way.Such determinations are of great interest in technical, biological andmedical terms and often are only possible by using specialized technicalmethods which have not become wide-spread. The following selectedexamples, according to the invention, may be mentioned: determination ofspermatozoa mobilities for fertility determinations, mobility ofmacrophages, activity of contractile elements, mobility of membraneproteins in natural or artificial membranes, mobility of actively orpassively transported molecules. Preferably, this is done by labelingthe cells, molecular complexes or molecules of interest with specificdye-labeled ligands, such as labeled antibodies or antibody derivatives,or by direct labeling with a dye label.

One critical advantage of the procedure according to the invention isthe possibility of screening pharmacologically active substances throughbinding of known fluorescence labeled ligands to receptors known per sewhich may be present on cells or natural or artificial vesiclestructures. Presently, a preferred direction of research in searchingfor receptor binding active substances consists in cloning certainreceptors, such as the family of protein kinase receptors, first andexpressing them separately. Then, these target structures areimmobilized individually, e.g. in ELISA plates, and analyzed using ELISAassays. To do this, a considerable amount of research and personnel isrequired to which the risk must be joined that a cloned and isolatedlyexpressed receptor changes or loses its functionality or specificity.

According to FIGS. 1, 2), it is possible in the case of the invention tocompletely omit cloning of receptors. Cells or fragments of naturalcells or cloned cells can be employed since receptors must only be usedin concentrations whose values are within the range of the reciprocalbinding constant for the specific ligand interaction. This alsosuppresses the risk of unspecific interactions with other ligands orreceptors that may occur with high reactant concentrations. Hence, thepresence of other receptors does not interfere with the assay.

If different cells/cell lines are used in an assay with a single type oflabeled ligand, differences in the functional behavior of the receptorsmay possibly also be distinguished through competition with mutants orvariants of the binding ligand. A differentiated receptor function withrespect to one and the same effector in different tissues appears to bea not unfrequent regulatory mechanism (e.g. TNF, kinines) (see FIG. 2).This effect can be used pharmacologically by employing selective ligandvariants which recognize but one receptor type.

FIGS. 26 to 28 show the use of the FCS method according to the invention

-   (i) for the determination of the behavior of a fluorescence labeled    ligand with respect to association with a receptor of the outer cell    membrane,-   (ii) for distinguishing between bound and free ligand, and/or-   (iii) for measuring ligand mobility in the case of a passage into    the cytosol.

Alternatives (i) to (iii) taken together are an example for employingthe method according to the invention in a dynamic laser scanningmicroscope with which three-dimensional imaging of the mobility of alabeled molecular species can be achieved, inter alia. From thedistribution of concentrations of a particular molecule thus obtained,conclusions about the localization of this molecule can be drawn. Thismethod also allows for an evaluation of the molecular state in therespective cellular or tissular compartments, such as e.g. associationwith compartmentalized target molecules (e.g. sense/antisenseinteractions with virus nucleic acids).

(i) to (iii) are examplified by the human epidermal growth factor (EGF)with a cell-bound receptor (EGF receptor) from rats. The cells bearingEGF receptors are NBD2 rat bladder cells derived from a respective tumortissue. The cells are surface-fixed on Petri dishes in PBS buffer(phosphate buffered saline). They had been grown beforehand in standardmedium until a confluent monolayer had been reached. The mediumcontained EGF labeled with tetramethylrhodamine. For excitation, laserlight of 500 nm wavelength of an argon laser (0.5 mW) had been chosen.The free EGF factor has a rotational diffusion coefficient ofτ_(Dfree)=0.145 ms. Its concentration was 6 nM. FIG. 26 a shows theautocorrelation function of free EGF.

After 30 minutes of incubation with the cellular monalayer, anautocorrelation function according to FIG. 26 b is found in the casethat the measuring volume comprised the region of the outer cellmembranes (see also FIG. 5). 88% of the ligand detected by measurementis present in the receptor bound complex with the related diffusion timeτ_(Dcomplex)=14.54 ms. This time is a quantity relating to the diffusionof the receptor in the cell membrane. With the diffusion timeτ_(Dfree)=0.145 ms, 12% of the ligand are covered. About one EGFreceptor is present in one space element. The related membrane surfaceis 0.5×10⁻⁸ cm². After 30 minutes of washing, the autocorrelationfunction shown in FIG. 26 c is found from which the following can beseen: about 0.5 EGF receptors per measuring volume still retain theligand bound with high affinity.

If the FCS measuring volume lies within the cytosol of a cell with aportion which at least predominates, then FIG. 27 is obtained (EGF inthe cytosol). 38% of the internalized EGF is hindered in mobility(either through binding to receptors or through the influence of aviscous medium) (diffusion time τ=3.3 ms), and 62% of the EGF has thesame mobility as the free factor.

FIG. 28 a shows the interaction of a DNA oligonucleotide having thesequence M13/pUC (−21) primer (5′-TGACCGGCAGCAAAATGT-3′) with viralsingle-strand DNA of bacteriophage M13 which contains the correspondingcomplementary sequence. The oligonucleotide is labeled with Bodipy(Molecular Probes) at the 5′-C₆ position. The course of the associationreaction with time was measured according to the invention in solutionat 40° C. The solution contained 50 nM of oligonucleotide, 50 nM of M13mp18 (+) DNA in 10 nM tris buffer, pH 7.5, and 0.18 M sodium chloride.The variation of the successive autocorrelation functions reveal thekinetics of association. Autocorrelation was determined after 0, 0.5, 1,2, 4, 8, 16, 32, 64, 128, 192, and 256 minutes. The diffusion time ofthe free primer is 0.17 ms, and 2.9 ms when complex-bound. FIG. 29 showsthe course of the association as experimentally revealed as % fractionof the primer in the associated complex. A reassociation rate of 0.07min⁻¹ results.

FIG. 28 b shows the example of autocorrelation of the labeled primerDNA. FIG. 28 c shows the autocorrelation function of a mixture of freeand M13 DNA bound primer.

Cells of a measuring compartment can be analyzed in situ and in anessentially nondestructive way. This is especially relevant forpharmacokinetic investigations.

19. Kinetic Reaction Parameters

The possibility to determine diffusion times in terms of fractions ofseconds allows to analyze the kinetic interaction of two molecules withhigh association constants and to determine recombination anddissociation rate constants. This is of special interest for thecharacterization of the interactions having high biological specificity,such as antigen/antibody, ligand/receptor, and the like interactions.Analysis of particularly slow processes with constants up to 10⁻⁶ s⁻¹easily possible due to the advantage of self-calibration inherent to themethod according to the invention (FIG. 19).

20. Detection of Single Molecules

The high sensitivity of the measuring method allows for the observationof single molecules during their motion through at least one detectinglaser beam. By using so-called “molecular funnels” in the form ofspecial glass pipettes having outlets of ≦1 μm, single molecules can bebrought by flux into a laser beam having a diameter of 1-5 μm. By theaction of electric fields, Brownian motion is restricted such that eachmolecule will pass through the site of maximum intensity of the laserbeam. The arrangement of the optical units with opposing detectors andimmersion optics makes sure very good photon flux as well as accuracyand efficiency of the detection of the luminescence emitted in alldirections of space (FIG. 6). For instance, the arrangement is usefulfor the analysis of the sequences of single DNA or RNA molecules withthe aid of exonucleolytic degrading (J. H. Jett et al., U.S. Pat. No.4,962,037), but also for the detection of single molecules provided withlabel and charge.

21. Detection of Single Molecules by Using Electric Molecular Traps inStationary or Alternating Field

Single ionized molecules can also be held in the observation volumeelement by forced directed translation in an electric field.Alternatively, single or repeated translation through the volume elementcan be forced. This is preferably done in an arrangement which is shownschematically in FIG. 6. A flux of molecules passes a larger samplevolume in the center of which the observation volume is located. By anelectric field which may be a stationary or an alternating field,migration of charged molecules through the observation element can beforced. In this way, molecules can be quasi-focused. This “molecularfocusing” is important in the case that only one or a few molecules arepresent in the total volume element which will have to be detectedquantitatively.

To do this, the sample volume is preferably fixed as a microdropletbetween the outlets of two microcapillaries as have been described by B.Sakmann and E. Neher. The capillaries are vaporcoated with a conductivemetal layer, preferably gold on chromium priming, which is in contactwith the aqueous buffer system at the outlets of the capillaries. Themeasuring element is located inside the sample droplet wherein theemergence objective of the microscope is in direct contact with thedroplet or the droplet is separated from the objective by a sheet.

Once a single molecule or molecular complex is detected in the measuringelement after having left the end of the capillary, kinetic data canalso be obtained. It is not very complicated to technically realize afield or temperature jump in the small volume element. If reactioncomplexes exhibit a Wien effect or have a sufficiently high reactionenthalpie, those parameters can be used in relaxation methods, e.g. todetermine reaction rate constants.

The principle of single molecule detection with carrier-free,electrically mediated concentration of charged molecules, such asnucleic acids, in the measuring volume is of great significance for theanalysis of single molecules in highly diluted solutions. Two aspectsare prominently important therein: the active transport according to theinvention of one or a few molecules from a larger sample volume of10-1000 μl into the measuring volume of about 10⁻⁹ μl means aconcentration by a factor of 10¹⁰ to 10¹² (FIGS. 20, 21).

One molecule per ml means a concentration of about 10⁻²¹ M. With aconcentration as described, this means a final concentration of 10⁻⁹ Min the measuring volume. Thus, as described in the section DNA analysis,hybridisation with simultaneously concentrated dye-labeled probes can beperformed with fast reaction rates.

This means a notable progress for diagnostics. In this way, diagnoseswith a sensitivity not realized hitherto can be performed, particularlywhile omitting enzyme-based amplification procedures and the problemsrelated thereto, such as risk of contamination by amplificationproducts. This is of special importance in bacteria and virusdiagnostics.

If the viruses or bacteria are present in diluted solutions and are notcontaminated with a large excess of accompanying nucleic acids that arealso negatively charged the analysis can take place without preliminaryseparation of contaminating nucleic acid. This is the case, forinstance, in forensic analyses when extremely small amounts ofbiological material is to be genetically analyzed. In clinical analyses,this is the case with cell free supernatants of body fluids, such assputum, urine, or plasma.

A large amount of accompanying nucleic acids may interfere with theconcentrating process and the subsequent hydridization. However, thenucleic acid can be preliminarily enriched, e.g. by means of specifichybridization methods. To do this, certain nucleic acids are extractedfrom a large volume, e.g. by offering a molar excess of solid phasecoupled counter-strand probes which preferably are not homologous withthe probe, and are thus separated from contaminating, accompanyingnucleic acids. Subsequently, the nucleic acids are released toconcentrate them in the measuring volume according to the invention.

In principle, other molecules can also be concentrated in the measuringvolume by means of the electric trap according to the invention. Aspecific character of being charged of the target molecule is requiredwhich is either an intrinsic property of the molecules, such as in thecase of nucleic acids, or a charge established by conditions of themedium, or a charge generated by reaction with a particular ligand.

In a preferred procedure according to the invention, the specificdye-labeled probe or the labeled ligand in detection reactions otherthan for nucleic acids can be construed such that the test molecules aretransported into the measuring segment, mediated by the electric field,only after the specific complex formation has already happened.According to the invention, this is achieved by the non-complexed probebeing uncharged or even bearing opposite charge with respect to thetarget molecule and the complex of receptor-target and ligand to beconcentrated in the measuring volume.

FIG. 30 shows the movement of charged molecules in a dipole trap.Variations of concentration and oscillations of negatively chargedrhodamine labeled dUTP molecules in water in a laser illuminated volumeelement are shown at an oscillating electric field with a field strengthof 10 kV/cm and a frequency of 4 Hz. The optical axis of observationruns perpendicular to the field gradient (see FIG. 6) The effect ofconcentrating the molecules in the measuring volume becomes evident.This concentration effect is cancelled in the moment when the field isswitched off and the molecules leave the observation volume element bydiffusion. Comparable results can be obtained by means of opposingmicrocapillaries as described in FIG. 6.

FIG. 31 shows photon showers of single rhodamine 6G molecules in water.By photon shower is meant the sum of the detected photons received whilethe molecule is present within the Gaussian measuring volume. Thus, thepossibility of reliable detection of single molecules with a singlechromophor has been proven. FIG. 31 a: 2.5×10⁻¹¹ M; FIG. 31 b: 4×10⁻10M. The channel time was 4×10⁻⁵ sec in each case=diffusion time; Gaussianmeasuring volume 0.24 fl.

22. PNA (Protein-like Nucleic Acid)

Particularly suitable molecules according to the invention are thosewhose behavior of binding to nucleic acids is an especially tight onebecause they are uncharged or even contribute to electrostaticstabilization of a complex through a charge opposite to that of thephosphate backbone. Molecules capable of hybridizing must notnecessarily have the chemical character of a nucleic acid. So-called PNAmolecules have been described which can be used according to theinvention to particular advantage.

In the case of a relatively long-chained nucleic acid target this can beachieved by the excess negative charge of the target moleculedetermining the electric charge and the electrophoretic separationbehavior and e.g. overcompensating the opposite charge of a probemolecule. In this way it can be achieved that the complexed targetmolecules are selectively concentrated in the measuring segment aftercompletion of the hybridization whereas the excess of labeled probemolecules is eliminated from the measuring segment.

For instance, the method according to the invention also allows fordirect detection of single virus particles in a volume of about 100μl-10 ml (corresponding to 10⁻²⁰-10⁻²² M) of serum fluid withoutenzyme-based nucleic acid amplification procedures.

For the nucleic acid based positive detection in serum samples servingas an example herein, the following requirements must preferably be met:

-   -   The mentioned amount of serum fluid must contain at least one        virion with nucleic acid (DNA or RNA) accessible for        hybridization.    -   The solution must contain a highly specific nucleic acid probe        according to the invention as a test reagent with fluorescence        labeling. The length of the probe must be chosen such that high        specificity with respect to the target sequence is ensured        because RNA molecules might possibly occur in the serum in high        molar excess.    -   When choosing the length of the probe, the stability of its        binding to the complementary RNA or DNA must be considered. The        dissociation rate ought to be below 10⁻⁵ sec⁻¹, if possible.        This means that the hybrid will remain stable for about one day        even after the free probe molecules have been removed, i.e. when        the equilibrium at a presumed concentration of 10⁻²⁰ M lies        entirely on the side of the dissociated molecules. According to        the invention, this happens when the free probes are diluted by        electrophoresis later, preferably to 10⁻²⁰ M.    -   When hybridizing, the probe must be present in so high a        concentration that association and hybridization take place        within seconds to minutes. According to the invention, low        concentrations can be used if the substances discussed below are        added to the hybridization medium to accelerate association.    -   The probe is chemically linked to at least one, preferably more        fluorescent dyes according to the invention. The electrophoretic        mobility of the free probe should be different from that of the        complexed probe. This can be achieved simply by making use of        size differences or differences in conformation or, according to        the invention, by using probe derivatives with a modified,        neutral or positive, charge character.

The analysis according to the invention takes place in the deviceclaimed according to the invention combined with a specializedelectrophoretic unit described in a preferred embodiment.

It consists of an electrophoresis cell with capillary outlet (diameterabout 10⁻³ mm) and is combined with the single molecule fluorescencedevice (FCS) according to the invention.

FIG. 12 schematically describes a preferred embodiment ofelectrophoresis cell. It contains (1) at least one opening for theaddition/collection of the sample to be analyzed and/or a washingsolution; (2) wall electrode; (3) ring electrode; (4) Neher capillary;(5) golded tip as an electrode; (6) droplet outlet; (7) laser beam.

The electrophoresis cell is filled with the measuring sample to which aprimer solution is added as accurately dosed as possible. Between thewall and ring electrodes, a voltage is applied e.g. over a time switchresulting in a concentration of probe and hybrid in the ring electrodewithin minutes. Thereafter, high voltage is preferably applied—againover a time switch between wall electrode and capillary tip. The lengthof the capillary should be such that from this point separation of freeprobe and hybrid will take place due to electrophoresis as properly aspossible. The free probe should appear at the outlet of the electrodewithin a period which is clearly different from the period after whichthe measuring impulse of the hybrid comes in so that at this time theconcentration of unbound primer is sufficiently diluted. Preferably, thesolution comes out as a droplet so that no back diffusion can takeplace. Both time spans: T_(s), after which the impulse of the free probewill appear, and T_(z), after which the impulse of the hybrid willappear, are fixed, if possible. The hybrid will appear in a microdropletat a given time and can even be detected in terms of single moleculefluorescence. Optical measurement can also take place before the exitfrom the capillary.

Detection of single molecules is difficult if the disturbing signalsfrom the free probe are too strong. Single molecules per ml means 10⁻²⁰to 10⁻²² M. Because of the reaction times, however, probe concentrationfor association must be about 10⁻10 M. In this case, the combinationwith electrophoresis according to the invention allows for a very muchsharper separation than with the described difference measurement of anunseparated mixture. In addition, the hybrid which is possibly formedappears within a volume, whose order of magnitude is ≦10⁻¹² l, at a timewhich can be accurately calculated, and thus it is well detectable forthe method according to the invention. By selecting appropriatefluorescence labels, fluorescence can be made optimal.

23. Device for Preparative Selection of Desired Labeled Complexes inTerms of a Single Molecule Sorting Method with or without Combinationwith a Molecular Trap

In case a molecule, molecular complex, virus, or cell has beenrecognized by FCS as a desired target molecule, the possibility existsfor direct preparative enrichment. This assumes that by electrophoreticmigration the respective molecule is present at a defined place at adefined time shortly after measurement and can be electrophoreticallyseparated there.

Measurement of Mobilities in an Electric Field, Running TimeMeasurements in Capillary Electrophoresis, Running Time Correlation,Sequencing

Through measurement of the mobilities of molecules or molecularcomplexes in an electric field, e.g. using methods of capillaryelectrophoresis, information about the nature of the molecules can beobtained. Thus, amino acids of a protein or peptide as products of Edmandegradation, for example, with fluorescent label can be determinedthrough this electrophoretic mobility. In recent years, sequenceanalysis of peptides and proteins has become increasingly important. Ithas been a critical breakthrough to use analytical amounts of a proteinin gas phase analyzers as commercially available by now. In this way,the proteins from single spots of two-dimensional gels (O'Farrell gels)can be sequenced.

The efficiency of this method could be significantly enhanced further ifthe sensitivity of analytical determination of the degradation productsin a subsequent capillary electrophoretic evaluation could be increased.Compared with conventional detection methods, peak determination by FCSin combination with running time determination (running timecorrelation) allows for surprisingly high sensitivity. Thus, analyticalamounts of peptides and proteins which can be obtained by capillaryelectrophoretic methods are sufficient for sequence determination. Asthe initial amount, a single cell may be enough to be able to performsequence analysis for a protein contained therein. On the other hand,the sensitivity of the method allows for the structure of asubstantially longer sequence of 2D gel electrophoretically separatedproteins, peptides or cleavage products to be determined.

An enzyme-based amplification reaction such as PCR cannot reach suchsensitivities without considerable additional steps. The known problemswith enzyme-based amplification relating to contaminations with highlyamplified products do not occur in the method according to theinvention.

The method according to the invention in combination withelectrophoresis is not limited to application for nucleic acids.Proteins and protein complexes or low-molecular chemical ligands canalso be provided with charge carriers that allow for analysis accordingto the invention. For instance, negatively or positively chargedoligopeptides can be coupled to antibodies prepared by recombinanttechniques in order to subject them to electrophoresis undernon-denaturing conditions. Thus, even lower virus titers can bedetected, for instance when antigen analyses of surface proteins areperformed which occur in large numbers per virion or are even secretedisolatedly into the serum.

A variation of the electric trap to detect single molecules is theincorporation of a quadrupole instead of a dipole. By applying analternating field in the plane of the quadrupole, a charged molecule canbe prevented, at appropriate field strengths, from thermally diffusingout of the quadrupole region. If two additional electrodes are arranged,according to the invention, above and beneath the quadrupole(sextupole), then charged molecules will drift, after an appropriatevoltage has been applied between the outer sextupole electrodes and theaverage potential of the quadrupole, into the alternating field of thequadrupole and be concentrated there.

The sextupole electrodes can be formed by metal coated glass surfaces oftwo microscope objectives. If a single molecule is present in the volumeof the sextupole of about 40 μl, then this corresponds to aconcentration of 4×10⁻²⁰ M. With a voltage of 100 V between thesextupole electrodes and the quadrupole plane (distance about 1 mm), anucleic acid molecule will drift into the quadrupole plane within aboutone second. The molecule now held within the quadrupole plane is presentin a volume element of about 6 fl corresponding to a concentration ofabout 2.5×10⁻10 M and an increase in concentration by a factor of6.4×10⁹. Its presence is proven by determining the number of molecules(N=1) and the diffusion time which is characteristic for this molecule.

The voltages and voltage differences actually employed in the quadrupoleand/or sextupole depend on the ionic strengths of the analyte solution.

When a position-sensitive detector is used (avalanche photodiodedetector), whose different elements represent different space portionsor quadrupole planes, the electric field gradients can be arranged,through a feedback arrangement between detector elements and the poles(electrodes) of the quadrupole, such that the molecule is always held ata fixed position within the quadrupole. This position is defined by therespective detector element.

24. Electric Trap

For convenience, the “electric trap” mentioned above is realized byarranging the measuring compartment with essentially equal distancebetween two positively (negatively) charged poles (electrodes) lying ona common axis which goes through the measuring compartment. In the planeperpendicular to this axis there are at least two and preferably fourelectrodes between which an alternating electric field is formed. Theelectrodes are arranged in such a way that they or pairs of them arefacing each other. To these electrodes a rotating alternating electricfield is applied in which the positively (negatively) charged moleculesare located. Due to the electric charge of the two electric polesperpendicular to the alternating field, the molecules are restrainedfrom movement out of this alternating field. When the double microscopeis used which has been mentioned above and will be described in moredetail later, the electric poles are preferably the supports of the twoopposing objective lenses in the common focus of which the measuringcompartment is arranged.

When the elctric trap is used in routine analyses, it is important thata target molecular complex get from a relatively large sample volume(10-100 μl) into the very small measuring volume for observation. Toachieve this, the charged target molecule is brought, for convenienceand according to the invention, over a large potential gradient into avolume element with zero potential out of which or inside which it canbe controlled by multi-polar fields, e.g. quadrupolar fields, e.g. forfixation in and/or controlled motion through measuring volumes.Preferably, this is done in a capillary with a length of severalmillimeters or centimeters (FIGS. 20, 21) which will receive the sampleand at one end of which a voltage of e.g. +100 (or −100) V is appliedand the other end of which lies at a potential of 0 V. The electrodelying at 0 V has a pinhole behind which there is e.g. a quadrupolaralternating field on a low voltage level (see FIG. 20). According totheir electrophoretic mobility μ=ca. 10⁻⁴ to 10⁻⁶ cm²/Vs, targetmolecules quickly migrate into the pinhole and then move on into thegeometrically adjacent quadrupolar field. The capillary is made of e.g.glass or quartz, if it is desired to superimpose electroosmotic effectson electric migration as is done in capillary electrophoresis.Alternatively, capillaries made of e.g. Teflon with uncharged surfacescan be used in which case electroosmotic effects can substantially beexcluded.

25. Fitness Determination of Variant Spectra in Large Sample Collectives

Within the scope of evolutionary screening assays, the method accordingto the invention is useful for the determination of the binding ofligands to molecules (proteins, peptides, nucleic acids, antibodies)which are to be selected. The extreme measuring sensitivity achieved bythe method allows, in particular, for analysis of highly specificinteractions, which are e.g. of particular physiological or biochemicalinterest. The interaction is measured through binding of a ligand orlabeled ligand or through competition of the unlabeled ligand with alabeled inhibitor. Thus, fitness determinations of variant spectra canbe performed primarily in large sample collectives.

Fitness parameters may be:

-   -   affinity parameters    -   kinetic parameters    -   enzymatic parameters under particular medium conditions of the        test.        26. Sample Carrier Systems for Genotype/Phenotype Couplings

In the analysis according to the invention and in the evaluation oflarge sample collectives of phenotypic variants it is critical that thecorresponding genotype, e.g. the encoding plasmid or the encoding mRNA,can subsequently be singled out to continue the evolutionary process.This problem is by no means a trivial one. The process will be the moresuccessful, the more selectively this singling out is done, that is themore precisely the corresponding genotype can be isolated withoutcontaminating it with sequences coding for useless phenotypes.

27. Test Cells

With medium sample numbers (<10,000) volume elements can be employedwhich are arranged in fixed spatial separation and are referred to astest cells hereinbelow. These can be parts of a sheet system comparableto those described for PCT/EP 89/01320, PCT/EP 89/01387, PCT/DE91/00082, PCT/DE 91/00081, PCT/DE 91/00083, PCT/DE 91/00704, whereinindividual volume elements contain samples in sealed sheet elements.From the sealed elements, phenotypes which have once been identified canbe isolated along with their encoding genes or mRNA transcripts bydirect mechanical access.

28. Microcompartmentalization

The method, according to the invention, of optical measuring andevaluation of variants in ultrasmall sample volumes also allows for verysmall total sample volumes in form of a microcompartmentalization whichcannot, however, be handled in a trivial way. This is true for bothindividual filling and selective emptying of the compartments to preparea genotype identified as being positive.

Microcompartments can be built up from regular and irregular porouscarriers, such as capillary elements arranged in the parallel asdescribed in the patent application DE 42 37 383.1, or flat carriersmade of porous materials such as glass with controlled pores orcapillaries whose volume elements are separated one-dimensionally withinthe capillary but of which pairs are in direct contact.

A particularly preferred form of microcompartmentalization is depictedin FIG. 4. Under an optically transparent flat carrier, the volumeelements present in a sample to be analyzed in the form of recombinantor natural cells or artificially vesicular elements with theirrespective phenotypes and genotypes are applied. In another embodiment,volume elements are established only during application to the carrieror thereafter. Gel or vesicle forming polymers, especially polymersbased on thermoreversible structures, such as caprolactam derivativepolymers, are especially preferred.

Application can be performed first from a homogeneous solution withsubsequent segregation of the polymers to form separate aqueous volumeelements, or through application of microdisperse droplets by means of apiezo-controlled microdispenser.

In the way described, the contents of cells can also be analyzed. Forexample, cells can be enclosed in the described vesicular structures andlater lysed at higher temperatures. In this case, at least partialmixing of the solution enclosed in the vesicles and containing reactivemolecules or molecular complexes with the contents of the lysed cellwill occur. Reactive molecules can be e.g. nucleic acid probes, enzymesor proteins which will undergo specific interactions or reactions, whichcan be detected and quantified by the FCS method according to theinvention, with cellular components. This technique is analogous with insitu hybridizations or cell specific protein staining.

Carriers for simultaneous fixing of nucleic acids and the phenotypicmolecular structures to be analyzed, such as those described in theapplication of K. Henco et al., DE 42 37 381.6, are also useful as apreferred reaction carrier to achieve genotype/phenotype coupling.

Of course, carriers such as those employed by S. Fodor et al. within thescope of the so-called AFFYMAX technology in which the genotype isdefined by its x/y position on the carrier can also be used.

29. Photomarking of Selected Phenotypes

One preferred possibility of adressing and marking of variants selectedaccording to the invention within their respective volume elements isphotooptical marking of their position by using the described analyticaloptics (FIG. 7) This may be done by reflecting in light of a wavelengthby which a photoactivatable coating on the surface of the carrier can beexcited to produce, e.g. by selective discoloring, a reaction productwhich is easily recognized. The light signal is activated if correlationanalysis indicates a given predefined valence of the respective volumeelement analyzed.

A conventional photoreactive coating can be employed therein. Anadditional light source, preferably also a laser light source, may beused, or the laser employed for analysis may be used. Discriminationbetween measurement and marking of the position by photoactivation canbe achieved e.g. by using a frequency doubler for the marking reaction.The x/y positions of desired elements can also be collected byelectronic data storage.

After marking of the positions on a carrier, the desired nucleic acidcan be obtained from the corresponding volume element, for example, bymechanical access.

30. Photoactivation of Selected Phenotypes and Genotypes

Instead of marking the selected volume element, marking of thecorresponding genotype itself according to FIG. 7 has proven to beparticularly useful according to the invention.

According to the invention, several alternatives are preferred:

-   (1) photoactivated attachment of the nucleic acids to surface    structures of the volume element,-   (2) photochemical activation of nucleic acid specific ligands,-   (3) photochemical inactivation of nucleic acids in all volume    elements except the positively selected ones.

Within the meaning of alternative (1), psoralen derivatives can beemployed, for instance, which chemically link nucleic acidcounter-strands to one another, as double strand intercalating reagents,under 360 nm light exposure. Such ligands can be chemically linked, forinstance, with the carrier surface (FIG. 8).

In this way, a sufficient number of phenotype encoding plasmid copiescan be attached to the positively selected surface segments during thescreening. Subsequently, all nucleic acids that have not been fixed canbe washed off. Then, the selected nucleic acids can be subjected to anenzyme-based amplification reaction directly on the surface.

Alternatively, the nucleic acids can be recovered by making use of thereversability of psoralen linking. This may be done, for instance, bylight of 260 nm wavelength. According to alternative (2), the nucleicacid binding ligands can also be linked to other molecular elementswhich allow for ready subsequent purification and separation ofundesired nucleic acid structures. This may be exemplified by: couplingof DNA or RNA recognizing ligands, particularly photoactivatablepsoralen derivatives or intercalating dyes, coupled to affinity ligands,especially biotin, avidin, streptavidin, immunoglobulin, oligopeptides,or oligonucleotides.

According to FIG. 8, after light-induced chemical linking of thosecompounds with DNA or RNA from the positively selected volume elementsit becomes possible to purify DNA and/or RNA from all volume elementstogether and simultaneously separate them from the nucleic acids whichhave not met the selection criteria. Separation can preferably takeplace by hydrophobic chromatography, affinity chromatography, or byusing magnetic particles, wherein the surfaces have appropriateproperties of binding to the ligand of the adaptor molecule. Preferredexamples of such specific coupling are: oligo-dT/oligo-dA,avidin-streptavidin/biotin, NTA-IDA/(His)₆ and similar known complexforming agents.

In the subsequent step, the purified nucleic acids thus pooled caneither be directly subjected to an enzyme-based amplification reactionor to cDNA synthesis, or can first be decoupled from the ligand byreversion of the photochemically induced linking.

In the sense of the invention, one could also think of selectivelyinactivating the nucleic acids which do not meet the selection criteriaof the analysis [alternative (3)]. This can also be done withcross-linking substances such as psoralens, wherein cross-linking willoccur in such a way that the structures thus cross-linked are no longercapable to be amplified in successive enzymatic reactions. However, onedrawback of this method is that inactivation must be accomplished quitecompletely because otherwise the enrichment factor for the positivelyselected volume units is adversely affected. In the methods ofalternatives (1,2), the yield of enrichment is not of prevalentimportance. By means of enzyme-based amplification methods, very lownumbers of copies can also be enriched to be covered according to theinvention. However, for most of applications it is advantageous if aslarge as possible a fraction of the nucleic acids from a positivelyselected volume element can be preparatively covered. This can beachieved e.g. by means of optics illuminating a larger volume elementthan the volume element considered in the analysis.

31. Fraction Analysis/Flow Injection Analysis/GC/MS Coupling

Flow injection analysis with coupling to analytical/preparativeseparation methods is of particular importance in coupling methodsaccording to the invention to methods of unsharp chemical or biochemicalreactions to find active substances or optimize (DE 43 22 147 andWO92/18645) chemically or enzymatically generated quasi-species.

As has been set forth above, the present method is particularly usefulfor the analysis and evaluation of molecular collectives which arecomplex in terms of number and have been preliminarily generated in anevolutionary process. Functional analysis of complex systems withmolecular diversity, however, is also of considerable significance incases apart from that. Diversity does not only emerge due to evolutivesystems in terms of replicative mechanisms just as compartmentalizationof subpopulations does not only occur in cellular or vesicularstructures.

In synthetic chemistry, very complex systems of different molecule typesare produced deliberately or unintentionally wherein a given kind ofcomplexity can also be selectively generated. Microorganisms or plantssynthesize a variety of secondary metabolites from which a great numberof pharmacologically active structures have already been derived. Withchromatographic methods, such as HPLC, FPLC, gas chromatography etc.,such compounds can be efficiently separated and isolated, as is wellknown.

The method according to the invention does not only make accessibleparallel analysis of mutants/variants from so-called replicativesystems, such as nucleic acids or proteins, but also those fromchemically or metabolically complex mixtures. Conventionally, to datethe procedure was to first purify complex mixtures preparatively inindividual fractions, to analyze them chemically and/or reveal theirstructures and, if possible, to make them enter biological assaysindividually in the form of pure substances.

Now, with the method according to the invention, preparative use of thefractions or individual materials, which are present only inanalytically small amounts at first, e.g. for pharmacologic assays canbe achieved. In a preferred embodiment of the method according to theinvention, the obtained fractions are directly linked to an FCS assay.Producing individual substances before they positively respond to therespective problem in FCS assays is omitted. Blind screening for activesubstances as presently performed can be replaced by the possibility toselectively investigate fractions containing active substances.

Analysis of functional compounds in complex mixtures of materials is anambitious task of pharmaceutic chemistry. Primarily, the complexmixtures of natural substances from microorganisms and plants alreadymentioned are known. Japanese institutions and companies have achieved alead in screening natural substances with respect to the other nationswhich is difficult to be caught up on by persistently, since the firstantibiotics had been introduced, establishing extended banks of purifiedsubstances with revealed structures which can be introduced into ascreening in each new assay. This is much simpler than cultivatingorganisms each time anew, especially since the risk of repeateddetecting, meaning double developments of active structures which areknown per se, is avoided in this way.

Due to its advantageous properties, the method according to theinvention can renounce on this proceeding and nevertheless allows foranalysis of very extended and complex mixtures, since individualmolecules are covered virtually as pure substances. One should rememberthat a single microorganism can synthesize more than one thousandcomplicatedly structured secondary metabolites some of which can only bepresent in small amounts and cannot be identified by their functions inan analysis of the entire mixture of an extract. According to theinvention, mixtures of substances from a microorganism or a mixture ofseveral microorganisms or plant extracts can be separated first e.g. bychromatography to test the individual fractions for the presence offunctional compounds preferably “on-line” in a capillary at the end of aseparation matrix (see FIG. 9).

The schematic FIG. 9 is explained hereinafter. According to theinvention, complex mixtures of substances can be analyzed throughcoupling with a chromatographic separation. After chromatographicseparation, a labeled reference molecule is added to the fractionscontinuously and at a fixed concentration, to which the specificallybinding target molecule is also added at a fixed concentration. Asdescribed in FIG. 1, the respective concentrations are preferably chosensuch that about 50% of the molecules involved form a complex, sopossible interfering substances from the separated mixture can bedetected with maximum sensitivity.

Thereafter, the combined samples pass the detection unit through acapillary flow tube. The fractions are analyzed for specificallyshifting the considered binding equilibrium.

Synthetically produced mixtures such as, for instance, mixtures ofdiverse substituted or unsubstituted alkyl residues in alkylationreactions, when complex synthon mixtures are used, can also beanalytically covered as described above. It is no longer necessary thento separate the compound formed from its reaction mixture and tocharacterize it after each reaction step.

In a preferred embodiment (FIG. 9), aliquots of the substance to beanalyzed for interference are first added to the individual fractionsbefore the mixture is contacted with a solution containing the receptor,in order that possible competition reactions can be measured.Alternatively, if a receptor is already occupied, a slow dissociationrate constant could complicate detection of a displacement reaction.Receptor displacements reactions which are slow allow for themeasurement of the change with time, i.e. of k_(diss).

32. Screening of Complex Mixtures for Biofunctional InteractionProperties with Concomitant Rough Evaluation of Parameters for PhysicalInteraction with Target Molecules

If a mixture of different substances is to be analyzed, according to theinvention, for properties of interaction with target molecules, e.g. inLC/FCS coupling, upper or lower limits for binding constants allowingfor corresponding quality evaluation of respective guide structures canbe directly estimated. This shall be illustrated by the followingexample:

10 μg of a mixture of substances is applied onto a LC separation devicecontaining 1000 substances in which the individual sought substance iscontained only in an amount of 0.1%. This corresponds to an absoluteamount of 1 ng. After separation of the fractions, this amount ofsubstance is present in a volume of 5 μl. With an assumed averagemolecular weight of 200 Daltons, this means a concentration of 10⁻⁶ M.If the target molecule, e.g. a receptor, is added at a comparableconcentration, then complex formation can be accomplished within a givenperiod of time only if the reaction rate exceeds a given maximum valueand the binding constant is >10⁶.

The detection reaction can be coupled to a parallel HPLC/MS or GC/MSanalysis in order to directly obtain structural data for the compoundsidentified as being active.

The small expenditure of substances of the analytical method accordingto the invention also allows for the use of the analytical methodaccording to the invention in competition with different alternativemethods of biosensor technology which can suffer from problems of signaldrifting when used in on-line analyses. Instead of the chromatographicunit described above, a sample dispenser may be used.

DNA/RNA Probe Assays

When the potential detection sensitivity of the technique according tothe invention is fully utilized, a specific problem arises in DNA or RNAprobe technique. On a molecular level, the detection reaction accordingto the invention requires the formation of double-helical structuresmade of single strand structures which are at least partiallycomplementary to each other, wherein the single strands involved mayconsist of DNA or RNA or mixtures of DNA and RNA fundamental structureswhich may bear chemical modifications, wherein said modifications inparticular may pertain to the base structure, especially those whichalter the luminophorous properties of the bases and/or those bearingsubstituents which have properties of specific binding to specificmolecules or molecular complexes and/or are luminescent substituents.

The formation of double-helical structures, however, is a relativelyslow reaction (hybridization, cot kinetics). In experimental practice,this means, for instance, that reassociation of genomic DNA from cellsis a process which will last for weeks and months, depending on theexperimental conditions, so that the experiment cannot actually becarried out completely.

Only repetitive genomic segments, which may occur e.g. in a numberof >100,000 per eukaryotic genome, can be rehybridized (Davidson &Wetmur).

An approximative formula which can very well be used in practicedescribes the reassociation of a denatured double strand fragment:t _(1/2) =N×ln 2/(3.5×10⁵ ×L×c ₀)t_(1/2) yields the half life of the reassociation in seconds at an ionicstrength of 1 M at T=T_(m)−20. L is the length of the probe fragment, Nis the length of unit sequence, c₀ is the molar concentration ofnucleotides, and 3.5×10⁵ is an approximative value for the intrinsicrate constant of the association.

Since the reaction rate depends on the sum of the concentrations of thetwo reactants (+ and − strands), there are two possibilities in generalto accelerate the reaction of reassociation. Since the excess componentdetermines the rate, in conventional blot assay the probe is usuallyused in excess to subsequently separate the excess probe in washingsteps. With the introduction of enzyme-based amplification reactions,such as PCR (polymerase chain reaction), it is also possible to amplifythe target nucleic acid to be detected to such an extent that it willdetermine the reaction rate. However, if amplification reactions areintended to be dispensed with in the method according to the invention,or the detection is to be performed without troublesome separation ofthe probe component in a one-pot procedure, one or more process stepsand procedures may be combined according to the invention.

The sensitivity of the detection of viral or bacterial pathogens in thegas phase (air germs) or in solutions or suspensions in small samplevolumes, as are sufficient for the detection according to the invention,can be increased by using simple filtration steps. They can be extractedfrom large volumes through filters or filter systems and incorporated insmall sample volumes. An alternative is concentration e.g. throughcoated magnetic particles.

For DNA/RNA analysis, probes with intercalating substituents can beemployed. The use of those chromophorous ligands is especiallypreferred, whose fluorescence behavior changes or is enhanced duringintercalation. Especially useful are substituents of the thiazole orangeclass. In the intercalated state, their fluorescence efficiency is about1000 times larger than in the free state. Thus, it is possible tomeasure a specific complex formation through intercalation at athousand-fold excess of non-dye-intercalating probe.

By using oligomeric or multimeric dyes linked to a probe, thesensitivity can be further enhanced by a factor of 10 to 100, since lessindividual events must be detected to produce the required signal.

Excess concentration of a double strand analyte is not necessarilydesirable to accelerate the reaction. Thus, an undesirable displacementof already associated probe from the complex may result if acounter-strand of the analyte present in excess hybridizes with thecomplex further up or down.

According to the invention, this problem is solved by taking care thatthe excess of analyte be present only in the form of a polarity withouta counter-strand, such as generated, for instance, by unsymmetricalpriming in a PCR reaction, or by runoff production of specific RNAsequences by means of RNA polymerases as naturally occurring in cells orbeing generated in homogeneous amplification reactions such as 3SR.

The displacement reaction can also be prevented by intercalatingsubstituents thermodynamically stabilizing the complexes (e.g. acridinedyes) or by initiating irreversible cross-linking (psoralen derivatives)(see patent application P 42 34 086.1).

If the use of a labeled probe in the range of 10⁻¹² M is possiblethrough optimization of the above discussed parameters according to theinvention and hence an analyte (counter-strand) in the range of 10⁻¹⁴ isstill detectable, then the reaction kinetics of reassociation (complexformation) becomes unacceptably slow. Using the approximative formulamentioned above, it can easily be calculated that a fragment of thelength and unit length of 200 nucleotides would take about 23,000minutes (16 days) to reassociate if 10 half lives should be waited outbefore the optical measurement by the method according to the invention.

By using a combination of organic solvents based on phenol andchaotropic salts such as thiocyanates or perchlorates, the reactionkinetics can be accelerated to about 100,000-fold (Kunkel et al.). Thosemethods have not proven successful in practice in filter assays. Theycan be combined, however, with the method according to the inventionwhich is preferably performed in solution. In this way, not only thereaction rate of the example mentioned above is shifted into the rangeof seconds, but the solution at the same time prevents degradationprocesses by the action of e.g. ribonucleases on RNA analytes.

The method also allows for the differential detection of large vesiclecomplexes as are necessary for a differential diagnosis in lipidmetabolism if distinction between different transport vesicles LDL,VLDL, and HDL is sought. Therefor, relatively complex electrophoreticmethods must be employed to date the quantification of which is noteasy. Dye-labeled vesicles can be distinguished according to theinvention by mobility and/or rotational diffusion measurements. Thevesicles may be stained with fluorescence labeled specific antibodies.Alternatively, fluorophorous label molecules can be specifically andpermanently incorporated in the vesicle structures.

Functional Assays of in vitro Translation Products

The use of the screening technology according to the invention is ofparticular importance for the analysis of replicative molecules in theform of proteins or peptides in combination with in vitro proteinbiosynthesis. In vitro protein biosynthesis avoids recombinant cellularsystems. However, the effectivity of in vitro protein biosynthesis is sosmall that detection of the function of the synthesis product is notpossible without expenditure. In average, no more than one peptide orprotein molecule is produced from an mRNA molecule. The result can beeven worse. The sensitivity of the method according to the invention,however, allows for determination of function since mRNAs must be usedin the synthesis mixture only in the μM concentration range and belowand a small sample volume is sufficient for the analysis.

Determination of Molecular Size Distributions

In the analysis of polymeric chemistry, it is important to determinepolymer distributions. This can be achieved in a simple way by using themethod according to the invention which hence represents an alternativeto ultracentrifugation methods and physical flow methods. Herein, theinherent fluorescence of an oligomer or polymer may be used orassociation or coupling of luminophorous ligands can be observed.

In situ hybridization is a method in which the specific double strandformation between a labeled nucleic acid probe and a complementarytarget nucleic acid is performed in a geometrically fixed arrangement ofthe object to be analyzed. The object to be analyzed can be a surfacefixed preparation of molecules or molecular complexes. Examples includepreparations of chromosomes, transcription complexes, or translationcomplexes. In routine analysis, surface fixed tissue slices or cellsfrom cell cultures are often important.

Dynamic Laser Correlation Spectroscopy

Due to its sensitivity, the method according to the invention allows forthe localization even of single hybridized or, in the case of ligandsother than nucleic acids, complexed ligands which are coupled to afluorescence label. The advantage of the method according to theinvention is based on the high sensitivity of the detection of singlemolecules. This allows for direct analyses where otherwise the use of anenzyme-based amplification reaction would be necessary or high localconcentration of target molecules would be required, such as in the caseof polytene chromosomes. The use of double or multiple labeling in themethod according to the invention whereby the relative position ofinteresting structures can be determined is also claimed.

The method according to the invention with confocal imaging of smallestvolume elements by using a pinhole aperture for the analysis of dynamicprocesses can be used, according to the invention, in combination withthe corresponding method used in a laser scanning microscope in order toobtain a high spatial resolution of structures. Whereas with the laserscanning microscope fluorescence intensity alone is used as a measuringquantity, the “laser correlation microscope” according to the inventionemploys the correlation function and the dynamic contents thereof in themeasuring element defined by the space coordinates (x,y,z) which isimaged two- or three-dimensionally (FIG. 10). In this way,two-dimensional (cross section) or three-dimensional images of thedynamics of a labeled molecule (rotational, translational diffusion,chemical kinetics) e.g. in a cell or in another biological object can bedepicted.

The schematic FIG. 10 is explained hereinafter. The organization inprinciple of the optics according to the invention is depicted. Thesample is contained in a sample holder which can be shifted within agiven defined screen by a two- or three-dimensionally controllable piezodrive. The respective related volume elements are analyzed for dynamicprocesses and as a whole assembled into a two-dimensional (crosssection) or three-dimensional image by a computer.

33. Determination of Epidemiologically Conserved Gene Segments

Through determination of the dissociation rates of hybrid doublestrands, homology estimations can be performed in analogy to thedeterminations of dissociation rate constants described above. This isof great importance in epidemiological analysis of diverging pathogensas in the HI virus. To develop diagnostic probes and to evaluate theirreliability, several gene segments of different origin must be examinedfor those parameters (see FIG. 22).

Method for Simultaneous Testing of a Plurality of Mutations on a TargetGenome

In the analysis of genetic diseases, the problem frequently arises toassay for the presence of a great number of possible mutationssimultaneously. This is the case especially with dominant geneticdiseases or X chromosome encoded diseases. With recessive diseases, itis often important to evaluate whether a particular point mutationoccurs only on one allele or on both alleles simultaneously (see cysticfibrosis with more than 30 mutations described to date). The procedureaccording to the invention allows for simultaneous analysis fordifferent mutations in one sample (FIG. 23).

Detection of Single Bacteria Through the Binding Specificities ofSurface-expressing Bacteria

For a great number of important applications of modern biotechnologicalresearch, it would be extremely advantageous and efficient, if in amethod detection of a single bacterium or virus with functional surfaceproteins could take place instead of the detection of a functionalbiomolecule in a given sample volume. The critical advantage lies in thecoupling, which is often very interesting, of a phenotypical expressionproduct, e.g. a natural or recombinant surface protein, to its genetictemplate.

The genome of microorganisms comprises about 10⁷ nucleotides. By shotgunexpression, subgenic fragments of an average length of 100 amino acidscan be expressed by methods known per se. Considering the variation ofreading frame (factor 3) and an assumed non-coding complementary strand,10⁸ recombinant bacterial clones contain each segment about 100-fold.10⁸ recombinant bacterial clones which are contained in 1 ml of asuspension of 10D can be examined individually for e.g. their propertiesof binding to IgE from an allergically responding patient by the methodaccording to the invention in about 24 hours. The bacteriacorrespondingly characterized will have to be singled out or at least tobe highly enriched, and to be biologically expanded, or thecorresponding genome segment will have to be amplified and characterizedby enzyme-based amplification methods.

Such problems are connected with methods for the evolutive optimizationof peptides and/or proteins by using mutagenesis methods and selectionmethods such as described, for instance, in WO92/18645. Within 24 hours,about 10⁹ bacteria can be screened by their properties of binding tospecific dye-labeled substances for the presence of a bacteriumexpressing a surface protein/peptide having the ability to interact withthe target molecule at a given concentration. The correspondingbacterium can be cloned from such a reaction mixture by conventionalmethods.

Another important application spectrum results from the so-called genomeproject for the functional mapping of gene segments from genomiclibraries, cDNA libraries or libraries of subgenic structural elements(Shape Space). In this way, the functions of genomic and/or subgenomicsegments from extended collectives, e.g. their behavior of binding totarget molecules, can be determined.

The use of the methodology described of functional assignment ofgenetically encoded peptide segments will become very importantespecially in allergologic research. The assignment of immunodominantepitopes on allergens (e.g. Aspergillus, milk protein, α-amylase) is ofextraordinary importance and represents a problem that has beendifficult to solve to date. Typical problems occurring in practice are:

The determination of the IgE binding molecules in a mixture ofsubstances which is usually ill-characterized. For instance, answeringto the question is important which contents of soya lecithin areimmunogen: the pure substance alone, the pure substance in itsinteraction with impurities of the preparation, or the interaction withstructures of the host organism. According to the invention, thedifferent substances in the mixture can be differentiated with labeledIgE from patients.

By expression of subgenic gene segments, the immunodominant epitopes canbe localized and characterized by the method mentioned above. With theseresults,

-   -   evolutively analogue functional molecules lacking the        corresponding immunodominant regions, e.g. a less immunogenic        α-amylase, can be generated by the methods described in        WO92/18645, and    -   the specific epitopes can be prepared simply by standard methods        of genetic engineering and be used as pure test reagents or for        desensibilization.        The Device

The measuring array is a device which is particularly useful forperforming the method according to the invention due to thediffraction-limiting focusing of a laser beam in the arrangementdescribed below. According to FIG. 14, the device is characterized by aprefocused laser beam. By introducing a combination of focusing lens andexchangeable microscope optics with constant imaging distance, thediameter of the prefocused laser beam can be varied. After deflection bya dichroitic mirror, the prefocused laser beam is imaged on the samplevolume which is present, for instance, on a carrier or in a hanging drop1 by means of air or water immersion optics with or without a coverglass. Usually, the fluorescence emission is taken up and imaged by theimmersion optics in an angle of 180° with respect to the direction ofthe exciting light. In the object plane 25, there is a pinhole aperturewhich is then imaged in an appropriate scale on a semiconductor detectorelement (avalanche photodiode) after passing appropriate cut-off orinterference filters. The appropriate scale results from adjustingimaging of the sample to the dimension of the photodiode. Preferably,the photodiodes are realized relatively small, as in the range of 100μm, so that they can “replace” pinhole apertures in terms of a confocaldetector. In a special embodiment of the device according to theinvention, the diodes can also be arranged in ensembles in the form ofdetector arrays.

Imaging of the pinhole aperture 50 can take place using a beam splitter60 on, for instance, 2 detector elements 53, 54 that are optimized fordifferent emission wavelengths. Instead of the pinhole aperture, one ormore semiconductor detector elements (an array), for example, can beplaced in the image plane.

In a preferred embodiment, the device according to the invention, whichcan be divided mentally into a unit for the generation ofdiffraction-limiting focusing of a laser beam and an observing unit, hasthe following construction elements. The appliance 20 for prefocusing alaser beam 21 further contains a dichroitic mirror 30 in the beam pathof the laser to deflect the laser beam 21. The laser beam generated bydiffraction-limiting focusing is imaged after deflection by thedichroitic mirror 30 by means of another lens 40 into the sample whichis positioned, for instance, on a carrier or is present in the form of ahanging drop 1.

Optionally, the observing unit has filter appliances 51, photon counterappliances 52, a correlation appliance 71 and/or a multichannel scalerappliance 72. The measuring signal can optionally be processed and/orevaluated in a computer assisted way.

FIG. 15 shows schematically the prefocusing appliance 20 for prefocusingthe laser beam 21. By the lens L 22 and an array 23 corresponding tomicroscope optics the collineated laser beam 21 is imaged on the imageplane B₁ through the lens 22. The array 23 images the laser beam onimage plane B₂ as a first image. Preferably, the array 23 is providedwith an exchangeable arrangement of lenses, for instance in the form ofa microscope nose piece. The diameter of the prefocused laser beam 21can be varied therewith.

In a preferred embodiment of the device according to the invention, thedetection unit consists of two detectors 52 and 54 and has a beamsplitter 60 partitioning the light 55 emitted from the sample to thedetectors 53 and 54. This arrangement is schematically shown in FIG. 16.It is advantageous therein, that the emitted light 55 from the sample 1passes imaging lenses 56, 57 and filter elements 58, 59 prior toentering each of the detectors 53 or 54. In particular, it isadvantageous that the detectors 53 and 54 each can detect light ofdifferent wave-lengths. This can be achieved by selecting suitablefilters.

If the detector elements are placed in the image plane in the form of adetector array, the use of the pinhole aperture 50 can be dispensedwith. The detector elements should then preferably have a size of <100μm. Another preferred embodiment of the device according to theinvention has a pinhole 50 in the beam path 55.

In FIG. 25, a double microscope as used for investigating a measuringcompartment (sketched out at 62) is depicted in side view. Themicroscope has a vertical support 63 (rectangular tube) provided with asole plate 64. On the upper end of the support 63, a central supportingarm 65 is pivoted to rotate around a horizontal axis. The centralsupporting arm 65 is devised hollow and provided inside with opticalelements, such as a beam splitter 66 and a 45° reflecting mirror 67. Thebearing axis 68 of the supporting arm 65 is devised hollow, wherein twosuperimposed laser beams are radiated axially into the supporting arm 56alongside the ideal rotation axis and there impinge on the beam splitter66 and on the mirror 67 (broad roof prism) in the beam path behind.Through the beam splitter 66 and the mirror 67, the two superimposedlaser beams are guided out of the supporting arm 65 on two opposingsides; at these sites, the supporting arm is provided with openings 69(glass cover plate).

The two laser beams 70, 71 leaving the supporting arm 65 impinge on thebeam splitters 72, 73 which deflect laser beams 70, 71 so that theirdirection is parallel to the axial direction of supporting arm 65.

At the free end of supporting arm 65, a supporting arm 74 is attachedwhich is arranged in such a way relative to supporting arm 65 that botharms together form a T-shaped configuration. At the front side ofsupporting arm 74 facing away from support 63 there are guidingappliances 75 for guiding longitudinal shift of body parts 76 which inturn bear an objective nose piece 77 with the objective lens 78. Therelative alignment of the two nose pieces 77 is such that the objectivelenses 78 are facing one another and are lying on a common optical axis,while between the two objective lenses 78 the specimen stage 79 islocated which in turn is held by supporting arm 74. Inside thesupporting arm 74 there is a double spindle drive 80 with two spindles81 having opposite threads. The spindles 81 are in thread-connectionwith arms 82 projecting into supporting arm 74 and connected to the bodyparts 76. Thus, when the double spindle drive 88 is driven, the two bodyparts 76 are moving, depending of the driving direction, towards oneanother or away from one another, so that the focuses of the twoobjective lenses can be joined.

A double guiding system is connected with each of the two displaceablebody parts 76. Each of those double guiding systems is embodied in formof a twin fish tail slide rail 83, 84. These slide rails 83, 84 arearranged facing the two ends of supporting arm 74 at the faces and areshifted along with the body parts 76. The two slide rails 83, 84 projectbeyond supporting arm 74 on both sides (side of glass slide and ofconnection with supporting arm 65) while being parallel to thesupporting arm 65. The inner sides that are facing each other areprovided with optical elements 85, 86 for prefocusing the laser lightcoming from the semitransparent mirrors or beam splitters 72, 73. On thesides of the two slide rails 83, 84 that are facing away from eachother, more optical elements (lenses, apertures, filters and the like)are located in order to affect the light coming from the measuringcompartment. 88 are the pinholes and 89 designates biconvex lenses forimaging the pinhole apertures on the detectors to detect thefluorescence radiation. Furthermore, at the outer sides of slide rails83, 84 that are facing away from each other, there are reflectingmirrors 89 being aligned in an angle of 45° and deflecting the lightcoming from the measuring compartment 62 towards the optical elements87, 88. In addition, the actual detectors 90, 91 (avalanche photodiodes)which convert to electric signals the information from the receivedlaser light required for further processing in cross correlation arelocated on those sides of the slide rails 83, 84.

The operation mode of the double microscope shown in FIG. 25 is asfollows. Through the bearing axis 68, the two superimposed laser beams(70, 71) of different wavelengths are entering supporting arm 65 whereone of the laser beams 71 is reflected by the beam splitter element 66by 90° to one side and the other laser beam 70 is reflected by 90° inthe opposite direction via the mirror 67 after having penetrated beamsplitter 66. The laser beams 70, 71 leaving openings 69 of supportingarm 65 impinge on the beam splitters or semitransparent mirrors 72, 73,from which they pass the optical elements 86. Thereafter, the laserbeams penetrate supporting arm 74, to which end the latter is providedwith elongated holes 92 on its sides facing the support 63 and thespecimen stage 79 (in FIG. 25, only the elongated holes 92 facingsupport 63 are depicted). Then, the laser beams 70, 71 further runthrough the body parts 76 where they impinge on equally semitransparentmirrors 93 from where they run through the nose pieces 77 and theobjective lenses 78 to impinge on the measuring compartment 62. Thelight reflected by the measuring compartment 62 penetrates thesemitransparent mirrors 93 without deflection and is sent to the opticalelements 87, 88 at the outer sides of slide rails 83, 84 by thereflecting mirrors 89. Thereafter, it impinges on detectors 90, 91.

In order to be able to adjust, depending on the objective lenses 78 usedwhich are identical, the focuses of those lenses onto the measuringcompartment 62, the body parts 76 and along with them the slide rails83, 84 can be shifted, as has been set forth above. Since thesemitransparent mirrors 72, 73 are held on the sides of the slide rails83, 84 that face each other, as are the optical elements 86, thedistance of the semitransparent mirrors 72, 73 from the reflectingmirror 67 and the semitransparent mirror (beam splitter 66) changes whenthe body parts 76 and the slide rails 83, 84 are shifted. In the regionsfollowing the semitransparent mirrors 72, 73, where the laser beams 70,71 are running parallel to the supporting arm 65, the distance of thosebeams from said mirrors is changed. According to this, their relativeposition within the elongated holes 92 of supporting arm 74 changes.From this it becomes apparent that all optics which are located outsidethe central supporting arm 65 are moved when the focuses of the twoidentical objective lenses 78 are changed while the two possibledirections of movement coincide with the directions of the laser beams70, 71 leaving the central supporting arm 65.

The entire double microscope has an extremely compact construction. Allelements are arranged such that the weights are “essentially uniformly”distributed. The operator of the double microscope facing the specimenstage 79 is not hindered by optical elements and appliances of themicroscope in his working area. The central supporting arm 65 and hencethe total of the optical appliances of the double microscope can berotated (see arrow 94.). The central supporting arm is held at thesupport 63 by two bearings which are tensioned axially to one another sothat no bending will occur. The position of one of the two objectivelenses 78 can be positioned with extreme accuracy by a piezoelectricallyor otherwise driven and working adjusting element (not shown) in orderto be able to balance an offset of the common focus of the two objectivelenses 78 from the position where the measuring compartment 62 islocated on the specimen stage 79.

In addition to the optical elements which are described and depictedherein, such as lenses, filters, reflecting mirrors, semitransparentmirrors, additional optical elements can be positioned in the beam pathof the laser beams 70, 71, if this is required or recommended by theexaminations to be performed.

FIG. 17 shows a deoxyribonucleic acid labeled with rhodamine. Theordinate exhibits the normalized intensity correlation function. Theabscissa is a logarithmic time axis. The concentration are given interms of labeled molecules per volume element (2×10⁻¹⁶ l). FIG. 17 a)shows the mononucleotide uracil, two molecules per volume unit, whosediffusion time is 0.067 milliseconds. FIG. 17 b) shows a DNA with 500base pairs corresponding to 0.3 molecules per volume unit having adiffusion time of 1.8 milliseconds.

FIG. 18 shows the interaction of a fluorescence labeled receptor ligandwith cell-bound receptors (β-adrenergic receptors) in human lymphocytes.The axes of the system of coordinates are as described in FIG. 17 above.FIG. 18 a) shows the labeled ligand in BSS, 10.7 molecules per volumeunit with a diffusion time of 1.1 milliseconds.

FIG. 18 b) shows the lymphocyte receptors labeled with ligand in BSS, 72molecules per volume unit, diffusion time 13 sec.

FIG. 18 c) shows the situation of 76% free ligands and 24% ligands boundto the lymphocyte receptor.

Since fluorescence correlation functions can be obtained within 10-100ms, 1000 picture elements can be coded within 10 to 100 seconds. Inparticular, each picture element of the method according to theinvention corresponds to one Poisson space element typically having aradius of 0.1-1 μm and a length of 1-3 μm. The correlation function iscalculated in each picture element for a given period of time and storedalong with the respective coordinate x,y,z. Thereafter, the preparationis preferably shifted by a piezo drive to the new coordinate point, andso forth. Instead of shifting the preparation, the laser beam, forinstance, can also be shifted within given limits by a suitable mirrorappliance (see FIG. 9). The dynamic picture elements are then assembledto an image in the computer.

FIG. 6 describes the preferred arrangement of the optical detection unitwith an electric molecular trap with respect to the sample volume andthe measuring volume. One or two detectors (detectors 1/2) detect theemitted fluorescence signals from the measuring volume element which arealso imaged confocally through one or two optical units as described inthe text. The aqueous sample is either in direct contact with thesurface of the emergence lens or is separated from the objective by athin sheet as depicted in FIG. 3.

The sample is held between at least two capillaries with an insidediameter of the capillary end of about 1 μm. In the case of functioningas molecular traps for ionic molecules, the capillaries are coated witha conducting surface layer, preferably gold on a chromium priming towhich a rectified or an alternating field can be applied. Controlling ofthe field is preferably done by a computer which is interfaced with theoptical detection unit and can regulate the fields in a defined mannerwhen an interesting molecule is entering.

FIG. 3 describes a preferred embodiment of the arrangement according tothe invention for screening large numbers of mutants for particularfitness parameters. Samples can be examined using an optical detectionunit according to FIG. 6. The samples are present in the form ofdroplets under a sheet-like surface which in turn is preferably incontact with the objective in terms of water immersion. The sheet canbear certain coatings allowing for selective binding of molecules fromthe respective samples to their surface. The samples can be regularlydeposited at defined positions, e.g. when using a microdispensingsystem, or in random distribution. To prevent evaporating of the solventfrom the samples the droplets may be surrounded by a protecting matrix,e.g. polymer structures or oil.

FIG. 7 schematically shows FCS tagging of selected genotypes. Ifparticular samples correspond to fitness parameters preselectedaccording to FIG. 3, access to the respective volume segments can befacilitated by the surface being provided with a photoactivable coating,which marks the position, e.g. optically, and allows for subsequentaccess to the sample.

Access to a selected volume segment or to molecules contained therein,such as coding nucleic acids, as shown schematically in FIG. 8, can alsobe achieved by photoactivating soluble reactants in the volume elemente.g. to react with a nucleic acid. Nucleic acids thus labeled can besubsequently isolated in a relatively simple way in order to subjectthem to further reactions, for example, a PCR reaction.

FIG. 11 shows a selection of possible assays according to the invention.“Ag” stands for antigen, but refers to the analyte in general terms,such as e.g. nucleic acid molecules for detection in double strandstructures as well.

“Ak” stands for antibody but refers in general terms to a specific testreagent for an analyte, such as antibody fragments, binding domains, ornucleic acids complementary to an analyte.

“F” stands for a luminescence dye, in particular a fluorescence dye.

-   (A) Specific complexing, according to the invention, of an analyte    “Ag” by a fluorescence labeled test reagent wherein the fluorescence    labeled test reagent in a complexed form is distinguished, according    to the invention, from its free form. This constellation allows for    an excess of up to 1000-fold with respect to the analyte.-   (B) Same as (A), however, the binding of a second test reagent added    in excess in an unlabeled form is used to increase too small a    difference in the sizes of the complex and the uncomplexed labeled    test reagent.-   (C) Competitive RIA-analogous assay with a smaller than equivalent    amount of test reagent and addition of fluorescence labeled    competitor analyte.-   (D) Assay with large excess of test reagent, wherein at least two    different test reagents are employed whose dye labels indicate    specific complex formation through energy transfer.-   (E) Same as (D), wherein the different dyes are detected    independantly according to the invention and the formation of a    common complex is determined by time correlation of the different    optical signals.

FIG. 19 schematically describes how the dissociation behavior ofcomplexes from n receptor molecules in n reaction mixtures and withdye-labeled ligand can present itself in parallel experiments. Indefined time intervals, several reaction mixtures are repeatedlyanalyzed. At the beginning, excess of an unlabeled ligand is added tothe mixture so that any dissociated complex is converted again into acomplex with unlabeled ligand. From the courses of curves 1,3,nindividual dissociation rate constants can be estimated, the courses ofcurves 2 and n−1 reveal two distinguishable dissociation processes andindicate distinguishable receptors.

FIG. 20 shows different embodiments of the electric trap according tothe invention. (a) a,b,c,d represent quadrupolar electrodes (metalcoated Neher capillaries or metal vapor deposited electrodes onmicrostructures on flat sample carriers (silicone, glass and other basematerials)); e,f in the case of sextupole electrodes (e.g. as metalvapor deposited emergence lens of one or two objectives). Adjustment isdone by x,y,z adjustment. (b) Use of flat carriers with etched electrodechannels or LIGA technique prepared forms through which the motion ofcharged molecules in the electric field can be controlled. The bottomplates for e and f can be objectives coated as sextupole electrodes ormetal vapor deposited coverings. (c) Use of (b) in combination with asample dispenser system consisting of a capillary made of mineralmaterials (e.g. glass, silicon, etc., or plastics such as Teflon toprevent electroosmotic capillary effects) for large volume samplereception with an electrode at the capillary end (about ±0-100 V) andwith a collecting electrode at earth potential (0 V).

FIG. 21 illustrates the possibility of detection of charged molecules bymeans of electric traps. (a) If target molecules are present within thequadrupole or sextupole field, the molecules can be set into forcedmotion by a random alternating field over the electrodes a,b,c,d. Theythus become countable according to the invention. (b) The position of amolecule within the trap is recognized by a multielement detector. Byactive feedback the quadrupole/sextupole field is adjusted such that themolecule gets fixed in its position within a defined area/volumeelement.

FIG. 22 schematically shows analysis for epidemiologically conservedgene segments on a virus genome. A DNA/RNA mixture of different virusstrains is labeled segment by segment each with a labeled counter-strandprobe and subjected to a displacement experiment by an excess ofunlabeled probe. The rapid appearance of free labeled probe below themelting temperature indicates that many strains have formed complexeswith the probe exhibiting many mismatches. In these regions, the strainsare evidently highly heterogeneous.

In FIG. 23, a method is depicted by which it is possible, according tothe invention, to deduce the presence of at least one of severalpossible mutations on a genome segment simultaneously through crosscorrelation. A mixture of unlabeled fragments is added to the DNA or RNAmixture to be analyzed. Hybridization of probe p with dye F2 mustcorrelate with the simultaneous hybridization of at least one probem1-m6 labeled with dye F1, if one of the sought mutations is present.Probes m1-m6 are each complementary to the mutated sequences and cannotefficiently form double strand structures with wild type sequences understringent conditions. Preferred concentrations for the nucleic acid tobe analyzed are from 10⁻¹⁰ M to 10⁻¹⁴ M, whereas the probes are offeredin a concentration of preferably from 10⁻⁸ M to 10⁻¹¹ M.

FIG. 24 schematically depicts the significance of small excitationvolumes (a), small measuring volumes (b) and small volumes in parallelmeasurements (c) according to the invention. (a) A section from anexciting luminous pencil without prefocusing is shown with imaging of asmall measuring volume according to the invention. A region is formedwherein photoinactivation of a dye label can occur prior to entering theactual measuring volume so that the effective concentration in themeasuring volume is lower than the actual concentration. This isprevented to a large extent, according to the invention, by illuminatingwith prefocused exciting light and imaging through a pinhole aperture inthe object plane. Thus, a Gaussian volume with Gaussian distribution oflight intensity is formed (b). (c) shows a section from parallelirradiated exciting luminous pencils with prefocusing with preferredimaging of small measuring volumes or successive illuminations andmeasurements of different volume elements with different spacecoordinates within the sample volume.

1. A method of assaying a molecule or molecules in a sample by laserexcited fluorescence correlation spectroscopy (FCS), comprising a)exposing a measuring volume within said sample to a laser beam, thereby,effecting fluorescence of a substituent when coupled to said molecule insaid measuring volume, wherein said measuring volume is arranged at adistance of ≦1000 μm from a laser focusing optic, b) measuring saidfluorescence using detecting optics, and c) determiningmaterial-specific parameters of said molecule based on the measuredfluorescence.
 2. The method according to claim 1, wherein said measuringvolume comprises ≦10⁻¹⁴l.
 3. The method according to claim 1, wherein aconcentration of said molecule or molecules to be assayed amounts to ≦1μM.
 4. The method according to claim 1, wherein said material-specificparameters are translational diffusion coefficients, rotationaldiffusion coefficients, excitation and emission wavelengths, life of theexcited state of said substituent, or combinations thereof.
 5. A methodaccording to claim 4, comprising determining a translational diffusion,rotational diffusion, or both said translational and rotationaldiffusion, and further comprising a functional evaluation of saidmolecule by determining the absolute number of molecules in saidmeasuring volume, determining variations, with time, of to absolutenumber of molecules in said measuring volume, determining specificconcentrations of structurally distinct ligands or ligand-moleculecomplexes in said measuring volume, or combinations thereof and derivingthereof thermodynamic binding constants between said ligands and saidmolecules, rate constants of recognition reactions between said ligandsand said molecules, rate constants of enzymatic processes involvingcomplexes formed between said ligands and said molecules, orcombinations thereof.
 6. The method according to claim 5, wherein saidmolecules or molecule-ligand complexes are ionic.
 7. The methodaccording to claim 5, wherein said molecules or molecule-ligandcomplexes are non-ionic.
 8. The method according to claim 1, wherein achange in said distance over a time defines an apparent diffusion timeof said molecule or molecules.
 9. The method according to claim 1,wherein said substituent is a chromophorous ligand, a luminophorousligand, or a luminophore-labeled ligand having spectroscopic parameterswhich are correlated with a property or function of said molecule. 10.The method according to claim 9, wherein said substituent is aluminophorous ligand having an extinction coefficient ≧30,000 with aquantum yield ≧0.1, or said substituent is a chromophorous ligand, whichcomprises one or more dye oligomers.
 11. The method according to claim1, wherein measuring takes place within a superimposed electric ormagnetic field, which is constant or varying with time.
 12. The methodaccording to claim 1, wherein ionic molecules or molecule-ligandcomplexes are forced through said measuring volume, or held in saidmeasuring volume by a rectified electric field or an alternatingelectric field.
 13. The method according to claim 11, wherein measuringtakes place within said electric field effecting an electric moleculartrap, and wherein a luminophore-labeled ligand bears a smaller chargethan, or a charge opposite to that of, a target molecule which forms acomplex with said ligand.
 14. The method according to claim 13 furthercomprising electrophoretic separation of free luminophore-labeledligands from specifically complexed ligands.
 15. The method according toclaim 14, wherein said free luminophore-labeled ligands are nucleic acidprobes.
 16. The method according to claim 14, wherein said specificallycomplexed ligands are nucleic acid hybrids.
 17. The method according toclaim 11 further comprising, prior to said exposing step, concentratingcomplexes of the labeled ligand and the molecule in a firstelectrophoresis step and transporting said complexes formed into saidmeasuring volume in a second electrophoresis step.
 18. The methodaccording to claim 1, wherein said laser-focusing optics comprises anemergency objective which is either directly in contact with the sampleor separated from the sample only by a transparent sheet.
 19. The methodaccording to claim 1, involving assaying a molecule or molecules in aplurality of samples, whereby said sample volumes are arrangedtwo-dimensionally on a membrane, sheet or wafer surface.
 20. The methodaccording to claim 1, involving assaying a molecule or molecules in aplurality of samples, whereby said sample volumes are arranged linearlyin a capillary system.
 21. The method according to claim 1, wherein saidsample comprises natural cells, or cells modified in vitro, orartificially prepared vesicular structures.
 22. The method according toclaim 1, wherein said samples are generated by a microdispensing system.23. The method according to claim 1, wherein an access to phenotypicallyselected genotypes on DNA or RNA level is made possible by the use ofphotochemically activatable reagents.
 24. The method according to claim1, wherein the molecule is a test substance, wherein the substituent isa luminscent-labeled ligand, wherein the material specific parameter isan interaction between the test substance and a pharmacologicallyspecific receptor, wherein the interaction correlates with apharmacological activity of the test substance, and wherein binding ofthe luminescent-labeled ligand to said receptor is a function of saidinteraction.
 25. The method according to claim 24, wherein thepharmacologically specific receptor is selected from the groupconsisting of natural receptors on their carrier cells, receptors onreceptor-overexpressing carrier cells, and receptors in the form ofexpressed molecules, or molecular complexes.
 26. The method according toclaim 25, comprising at least two types of receptors, whose differentialbinding potential is determined through interfering binding of variantsof potentially pharmacologically active substances and aluminescent-labeled natural ligand.
 27. The method according to claim25, wherein the cells are capable of dividing or are metabolicallyactive.
 28. The method according to claim 24, wherein said substance ispresent in complex natural, synthetic, or semisynthetic mixtures, andsaid mixtures are subjected to chromatographic separation into samplesprior to said assay.
 29. The method according to claim 1, wherein themolecules are homologously complementary nucleic acid molecules, whereinthe substituent is a labeled nucleic acid probe coupled to the moleculesthrough hybridization, and wherein the material-specific parameters aretype, number, or both type and number of the nucleic acid molecules. 30.The method according to claim 29 wherein an excess of said labeledprobes is provided and said labeled probes are single-stranded syntheticor cellular RNAs or DNAs with a particular polarity (+ or − strand). 31.The method according to claim 29, wherein the reaction rate of complexformation in hybridization is accelerated by performing the assay in amedium containing chaotropic salts, or organic solvents, or bothchaotropic salts and organic solvents.
 32. The method according to claim29, wherein the degree of complementarity of the hybridized nucleic acidis analyzed through the thermodynamic stability of the complex.
 33. Themethod according to claim 29, wherein the detection of a complementarynucleic acid is quantified by i) using an internal standard, whosesequence differs from the sequence of the nucleic acid to be quantifiedin at least one point mutation and ii) performing the analysis at atemperature at which the different conformations of the complexes of theprobe with the internal standard and of the probe with the nucleic acidmolecule to be analyzed are distinct with respect to translationaldiffusion, or rotational diffusion, or both the translational diffusionand rotational diffusion.
 34. The method according to claim 1, assayingtwo different molecules together in one sample through a reaction of twodifferent ligands which are labeled with different dyes, wherein thedyes are either excited with light of different wavelengths ofindependently detected by light of different emission wavelengths. 35.The method according to claim 1, wherein the molecule is complexedsimultaneously with two ligands which are each labeled with opticallydistinct fluorescent dyes and the simultaneous complex formation isdetected either through formation of an energy transfer complex,correlation in time of the signals having different wavelengths ofexcitation, correlation in time of the signals having differentwavelengths of emission, or combinations thereof.
 36. The methodaccording to claim 1, wherein the molecules are vesicular structurescoupled by staining the vesicles with a substituent consisting offluorescent-dye labeled antibodies, or incorporating a substituentconsisting of luminophore-labeled ligands specifically and permanentlyinto the vesicular structure structures by specific and permanentincorporation, or a combination thereof.
 37. The method according toclaim 36, wherein said vesicles bear lipids of the VLDL, LDL or HDLtypes.
 38. The method according to claim 1, wherein the molecules areproducts of an in vitro protein biosynthesis and wherein the materialspecific parameters of the molecules are specific binding properties orenzymatic properties.
 39. The method according to claim 1, wherein themolecules are mixtures of different oligomers or polymers and whereinthe material specific parameters of the molecules are averagetranslational diffusion coefficients, or average rotational diffusioncoefficients, or both average translational diffusion coefficients andaverage rotational diffusion coefficients.
 40. The method according toclaim 1, comprising a three-dimensionally compartmentalized sample to beassayed, wherein the dynamics or reaction kinetics of particularmolecules in a plurality of measuring volumes as well as the positionalcoordinates of said volumes are registered in order to assemble a two-or three-dimensional image thereof.
 41. The method according to claim 1,assaying samples for complex formation between unlabeled ligands andmolecules in competition with luminophore-labeled ligands whereinassaying is performed i) in solution, ii) by coupling of molecules to asolid phase or iii) by using cell-associated molecules.
 42. The methodaccording to claim 1, wherein measuring said fluorescence usingdetecting optics occurs at measuring times of ≦500 ms.